Of those 2 systems i would choose the Trane.
1,2 As long as the install, and Start-up are done correctly then either system will be reliable.
3, To the home owner they all do the same thing. We preference due to cleaning procedures etc.. Have a maintenance contract on your unit, and we inspect that no tubes are rubbing to ensure no leaks. Trust me Maintenance is a very big thing now with the high efficiency units.
4. A VS blower will not be problematic at all, but a VS blower will not solve ductwork issues! Dip switches can be adjusted to help airflow though.
5. Yes, its a very good filter. He probably recommended the F100 because it has a Merv rating of 10 which is very good airflow for the type of filter you want. A HEPA filter which does the same thing would be upwards of 14 or 15 Merv rating. You ductwork may not be able to accommodate that.
6. I am not sure what your asking.
I also like the fact he's replacing the Line set instead of Flushing it! I think you have a reputable contractor here. In my opinion that is the correct thing to do if at all possible.