Yes - probably a bad idea.

I agree with Joe that 3 tons is likely right. I question the premise that a 3 ton would run 3800 hours in winter if the load calc is accurate.

Enlarging the ducts to accommodate airflow needed for a 4 ton unit to actually perform at rated efficiency could cost way way more than the few extra hours of aux use occasioned by installing the three ton.

A charlatan (hack) might attach a 4 ton unit to a 3 ton duct system. The 4 ton might then actually produce 3.25 tons or so of heating at much lower efficiency and greater noise. Duct limitations trump nameplate tonnage every time.

Use of 65 vs 69 degrees on the heat loss calc is likely a minor difference.

If you don't trust your contractor there will be no piece of mind. Check references ask, municipal inspector. Don't miss the forest for the trees.
You are leaning toward the opinion of guys who do not do their job correctly.
Check weather data with local airport to verify bin on software.
A two stage unit is supposed to run alot, cooling dominated climates don't have auxiliary so they must uneconomically design for 100% of load. Around 31 degrees F 2nd stage kicks in. That is not the same as continuous operation. 98% of load met is great.
Reducing fan speed to compensate for undersized ducts reduces efficiency.
I strongly encourage you to shop the contractor more than the design.
JMHO
j

do you think there would be any advantage to putting an extra loop in the ground? I notice in geodesigner that the extra loop does a bit to gain in the output of the system, with such long runtimes would the extra loop be a good idea in order to ensure that the loop temp stays in the proper range or would it be a waste of time

Understand I'm not trying to sound terse, but there is an advantage to many things. There are also disadvantages in ROI.
How many installs have each of these contractors done?
If you told me #4 is using you as an alpha project I would be more concerned. If you told me the bin report didn't accurately report your temps I'd be more concerned. I still don't know why your weather is warmer than mine.
Does an extra loop offer much more benefit? Not if the numbers you have provided are accurate. 98% is the highest I shoot for, not a starting point.
j

http://www.weather.com/outlook/travel/businesstraveler/wxclimatology/monthly/graph/USMI0477?from=36hr_bottomnav_business http://www.weather.com/outlook/travel/businesstraveler/wxclimatology/monthly/graph/CAXX0321 if you look at those two charts you can see that the bin data is likely correct, the temps for your area are much lower than mine, especially the max high and low temps. The question I have though is if windchill matters because those numbers on the bin graph are all without windchill and we could probobly drop another 20 degrees with wind chill out here

Wind matters, precipitation matters, sunshine matters.......
Do you think no one thought about this when desigining our software?
I can't tell you any other way. You are worried about the wrong thing.
Have you answered my questions about the installers?
Do you realize you've spent more time testing my opinion than answering my questions?
It's free advice, do with it what you will.
Joe

I am sorry I don't know much information about the experiance of the installers. I do know they have all installed geo systems before but I am not sure how many each have done. I had a fifth guy come out today who is doing another heat loss calculation of his own so we will see what he comes up with

oh I was also wondering, people seem to indicate that you should size your system to 70% but I am not sure what that 70% means...is it 70% of the overall btu requirement of the house?

We are Buffalo installing Geosystems, Based on the calcs, 47K BTU a 3 ton system should serve you well. Surprised only 1 guy did Manual J heatloss. We do it with every job, it really is not so much effort, and sometimes we get surprises. Let me know if you want us to look at it closer, you are only 30 min away.
I don't want to be the 6th guy bidding on a job, but I am happy to help.
www.buffalogeothermalheating.com

naw thats ok, I had another guy come in, he did a heat loss also and came up with around 49500btu and recomended a 4 ton unit and everything he said seemed like he was going to install it properly so we went with him. I know a 3 ton would likely do it for me but I want to have room in case in the future we add a little to our house or get a very cold winter. Since it should be adequate we also opted to have him leave out the plenum heater for now and will use our fireplace if we need a bit of extra heat

THE MOST IMPORTANT THING TO YOUR GEO SATISFACTION WILL BE QUALITY OF THE INSTALLATION. You will do what you like, but I hope you at least check the installers' references.
We offer advice here for free and you are of course free to ignore it (as you have). Elimination of the auxiliary coil ultimately causes less efficient operation (case I'm looking at right now has 3.64 average COP with a 5 ton and 3.72 COP with a 4 ton).
That doesn't mean you won't be happy with your system, but would you share with us predicted operating costs, and average COP's for the proposed 4 ton and the comparison to the 3 ton if it was provided.
Are you purchasing a one or two stage unit?
J

Geolink gives numbers that agree with the #4 quote - even up to a 52K design load.

...and behind door #4 is a 3 ton unit, if my review of the thread is correct.

two stage unit. The guy we went with did an open loop for a friend of my families and they were very pleased with the job. The others never offered any referances and since we knew a person who had this guy do an install we felt more comforable with that. everything he told me he would do seemed like he was out to do things properly. He was going to put the pipe at 6 feet instead of 5 feet, he was going to put the pipes 3.5 feet apart instead of 12-20" as the other estimates did, he was going to add another return duct but unlike the others who were going to put it in the basement he said it would be best to put it in the cold half of our house (on main floor) which has no return currently and will do that in the price as well. I downloaded the climatemaster software and entered the values into there. The estimated operating cost of a 4 ton unit of course depended a variety of factors but on average was only around $30-40 per year cheaper than the 3 ton. Basically the guy who suggested the 3 ton unit said that there would be no reason to do it because it wouldn't ever pay itself off over the life of the unit (I think the differance in install cost was around $1500). Of course that doesn't take into account that the guy who is doing it is charging $20003 plus GST for the 4 ton unit installed and the guy who suggested the 3 ton unit was around $22600+GST for a 3 ton so in reality the 4 ton was cheaper anyway. They are not the same brand though. The 3 ton suggestor sold next energy (rebadged climatemaster) and the guy who we went with sold Boreal (rebadged Nordic) both of which we have heard good things about just from research on the internet

Not heard anything bad about Nordic. Cheaper....ok why not.

also I am not sure what exactly is involved in a manual J calculation but the 3 ton estimate guy did measure doors and windows and what not and then had a paper that he filled some numbers in on to get his estimate. The guy who we decided to go with also did a calculation by measuring doors and windows and measured the house but his went into a computer program that took the direction of the windows and other things into account also.