Well if the manufaturer reccomends you only do a vacume test, that is meeting their spec, and you should probably follow the manufacturers reccomendation. As to the flare, it is a compressed metal on metal seal. They either work or they don't so a pressure test isn't going to tell you much else IMO. What exactly would you be looking for with a pressure test? Dosn't leak or dosn't explode
How high would you test it? What if you make a mistake? Since the manufacturer dosn't reccomend it, you would probably be on your own for any failure you discover, even if it is with their assembly...
Yes, the nitrogen would be evacuated with the deep vacume, just as the 80% nitrogen 20% Oxygen mix you are breathing now would be... Why do you pull a vacume? Well to get the non condensables out(better efficiency), but It is not so much to get the Nitrogen/Oxygen out of the system, as to get the moisture it carries with it, out of the system. The refrigerant reacts with the moisture(and heat) and creates acid which will eat the system from the inside out.
Now purging the system with low pressure dry nitrogen is not necessarily a bad idea. IE: inject low pressure dry nitrogen in one port and release it from the other port. This will dispace most all of the air currently in the system(and the moisture it is carrying) and the dry nitrogen passing thru wil readilly absorb any excess moisture. Just do it slowly so as not to cause overpressure or displace any oil... Then when you are evacuating you will be pulling out only the dry nitrogen.
The purpose of the schrader valve is to hold the system static while you remove the cap and attach a hose or vis versa. It prettymuch should be in place and a hose end designed to activate it used to open the valve when the hose is attached. If you pull a good vacume then disconnect the hose with no valve attached, you will suck a bunch of moist air back in, defeating the reason you evacuated in the first place. Or if you pull a vacume and then release the refrigerant, you will loose a bunch of refrigerant when you disconnect the hose, install the valve then cap the fitting... With the schrader valve in place, if you disconnect the hose with a vacume pulled, it may pull a little air back in as the schrader mainly is designed to hold pressure in the system. The best way is with the valve installed and using the proper hose end to activate the pin on the schrader valve. Confirm you have a vacume on the system and not on just the manifold, close the valve on the manifold and see how long it takes to pull a full vacume on just the manifold and hoses. Now open the manifold valve and watch the pressure rise as the system plumbing is connected to the manifold via the scrader valve fitting. IF you get little or no rise the schrader has not been activated by the hose end and you are not connected to the system. If it has been properly connected, you will see a considerable pressure change when you open the manifold valve, and it will take you considerably longer to re-pull a vacume due to the added system volume you are connected to and must now evacuate. Once you are happy with the depth and duration of the vacume, you can close the manifold valve and release the refrigerant into the evacuated system. Once this is done, the system will now be under positive pressure and you can remove your hose from the test port/fitting. The schrader valve shuuld retain the pressurized refrigerant in the system and you can install the fitting cap...
Not sure how your zones are configured, but the manufacturer should have a process to be followed... When in doubt UNDERSTAND and folow the instructions, especially if you want any chance at a warranty claim if it should become necessary.
As always, this is worth exactly what you paid for it
Good Luck