Congratulations on your new house.
I will start by saying I have merv6 pre-filter and merv10 high effeciency filter just as you describe. Were I having allergy problems I would go up to 8 & 15. I had/have benifit of air flow and tempature differential testing which shows there is no concurns with restriction. What those who rally against good filters fail taking in to consideration is that if you pull a pleat filter out flat,there is a lot of surface area.
1) Is this the installing contactor advocating the removal of pre-filters?????? I would think the collective square inches of pre-filter would alow free flow unless the returns are under size to begain with. The only way to know is by calculating minium return size then compare to what is in place. 10 to 15% extra return size is prudent just as insurance in case of mistake ( such as omitting a turn in data) while calculating duct work. The installer should have done the calculations. If a secound contractor is challenging those,you need more and different help than can be found on the net. Don't waste money on cheapies.
2) I see no advantage in removing 1 or 2 while leaving another in place,unless the single remaining filter is in an exceptionaly dirty area.
3) There is no "rule of thumb"interval. You can establish your model through inspection of the filter(s). On a pleated filter,the bottom of vees will collect 95% of impurities starting out. As time passes,you can easyly see the grey collection creep from bottom of pleat toward top of pleat. The filter should be changed before the upper 1/3rd of pleat is covered in enough dust to hide the color of filter.
The time required for that transisition on 5" will be much longer i you choose to use pre-filters.
There is a very real possibility that the installing contractor put filters in the intakes to prevent construction materials getting into returns. It is possible he intended to abandon the 3 intake filters after home was complete. Discuss this with the installer to get best answers.

klem1:
There is a very real possibility that the installing contractor put filters in the intakes to prevent construction materials getting into returns. It is possible he intended to abandon the 3 intake filters after home was complete. Discuss this with the installer to get best answers.

Yes that is exactly what the installing contractor did - to prevent any construction dust from entering the HVAC system prior to final delivery. He basically didn't install the 5" media filter until the house was basically transferred to us.

So back to the questions:

1) Yes - the installer is telling us to remove the 3 air return filters because in his words; "the system is running a race with one nostril."

Are you saying not to do it?

I will not secound guess the installer who is aware of all factors envolved. The 5" filter puts you light years ahead of most homeowners with 1" fiberglass filters so you are not likly to have problems with filteration.

@klem1 - I appreciate your clarification. I wasn't sure originally what your comment for #1 was leaning towards. :)

Cheers.