How much safety factor should be put into an air conditioner system?...

The answer is NONE!

Often AC contractors purposely oversize a system to avoid homeowner complaints that they can't get cool. This has simply passed the problem from one area to another or swept the dirt under the rug.

The ACCA manual which is the design basis for air conditioning contractors states there should be no buffer factor. That means AC systems should be sized and designed on a tight ship aka your contractor has to know what they are doing. In today's market of untrained technicians working on commission and shotty practices this is rarely found.

Design considerations should be:
Location and climate
Room size and location
Sq ft
Number of bedrooms
Shading
Orientation
Insulation
Windows

If your contractor is not measuring and noting these they are not doing a complete job.

Rules of thumb worked fine for leaky houses, but as houses have become tighter the AC system should get smaller as well.

This requires contractors to do something that probably hasn't been done in a generation and has somewhat become a lost art of designing and properly sizing an AC system and ductwork.

Each room needs to have the proper velocity, airflow and mixing of airflow and this has to be designed. Returns should be placed centrally and placed where an average room temperature is measured.

There are definitely more challenges but I would argue there are equal opportunities
for all parties and everyone benefits.