The easiest way to make a part transparent is to give it a MATERIAL with an alpha value of less thatn 100 (%).  0 is completely transparent, 100 is completely opaque.

Hint - in you VC (inside) model, either don't add "glass"  or give it very very low alpha..afte rall, you want to SEE out the windows.

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Well that's up to the creater and how your design methods differ. I will stick to gmax, because I know it has a wide envolope to play around with modeling and the texture properties along with animations. To really answer that question you would have to try it out and see which is easier to work with. But really Both programs are well capable of the same outcome, it's just which is easier to work with.

IF you're already working with gmax, stay with it and learn it.  FSDS is easier, but doesn't have as many powerful tools as gmax.  Just because *I* (and others) find FSDS easier doesn't mean you (or someone else) will.

With FSDS3 going through makemdl, there is common ground - we've all got to learn makemdl's "quirks".

FSDS makes getting a model into flightsim a LOT easier - (okay, with "practice" and shortcuts, someone with gmax can do the same thing), but with a couple of button presses, my model is sitting on the runway in flightsim, ready to take off - textures copied to the folder, at least the basic flight dynamics, etc etc., things that I'd have to do manually when I compile from gmax (of course, I cheat -  I compile the basic plane from FSDS and then just compile an MDL file from gmax to replace the original FSDS one...  )