I live in Miami and as part of a remodeling, I am replacing the entire HVAC system. When doing load calculations my contractor insists that he should use "worst case" calculations. Everything I've read points in a different direction, but I am unsure how much "safety factors" should be incorporated.
I am trying to have the most efficient house possible with low e windows, white roof, r-30 roof insulation, etc., but I fear if the calculation is not done correctly all this is for naught.

When I asked my GC to use the Manual J and Manual S, he said that these methods (which is not typically used) is the Prescriptive Method; hence Florida Code 403.  This method is more rigorous and does not have the safety factors which I spoke earlier about and are allowed with the second method. The second method is the Performance Method (Simulated Performance Alternative); hence Florida Building Code Section 405.  This is the method we typically use to calculate and design the HVAC system.  This was the method used to prepare your calculations and ultimate HVAC design which falls within typical design parameters for a single-family home of this character.

What method should I ask them to use?

Thanks for your thoughtful replies.

In warm climates--I think you qualify--solar gain and infiltration/air changes are weighted factors and can't be ignored. A blower door test is the surest way to determine the air changes and once plugged into a Manual 'J' program will give the experience designer all he needs for a very accurate heat load. Worst case is not a technical HVAC term, nor a wise use of data--if it is used at all.

The design temperature for Miami is 90°F. The target rH should be ,55%. Nothing should be added to any Manual 'J', for fudge, safety or worst case. Those margins are built in and adding to them will result in higher indoor humidity at best.

The designer should model the house on solid Manual 'J' software such as Wrightsoft, which will account for old construction and new upgrades such as windows, awnings and insulation. In hot climates the quality of sun-exposed windows can make a significant difference in the heat loads. Look up SGHC and buy accordingly.

Everything else is just so much hot air.

Remember, the worst thing that can happen when you under-size cooling is the temperature goes slightly above design--normally 75°F--but remains dry ,50%rH. If you over-size the cooling the worst case is short-cycling of the compressor in all but "worst case" weather and higher rH as a result.

One comment you made was about trying to have "the most efficient house" yet you site low e and R30 which are code monimum now. This doesn't qualify as out of the ordinary but if you think it does it can trash any calculators product.
get a good energy advisor and start first during the build to truly make your house efficient.

Note that even when "perfectly" sized, you will have periods of 75F and 95% humidity - so the system will sometimes be severely over-sized and typically won't do well with dehumidificaton. So variable speeds, a standalone dehumidifier or other dehumidification features are a good idea.

Even if you are comfortable enough (perhaps 70F@80%), < 60% humidity for at least a few hours/day is a good idea for mold reasons.

Note that parties and cooking can add lots of load. Perhaps at some point, you just throw in an extra, low cost mini-split to handle unusual loads.

Not necessarily over-sized just limited to ambient controls. The answer to mild temperatures and high humidity is, as jonr suggests, efficient dehumidification such as an Ultra-Aire.