Gain/Trim should most definitely be calculated when bouncing ("Apply Effects" is essentially a bounce-in-place). Not doing so, as you point out, would wreak havoc on level-sensing plugins. Can you suggest a test scenario that shows this not being the case?
 
For example, if you insert a compressor and note the maximum peak value in the track, the peak value should be unchanged after applying effects. 
 

Bit, I made a scratchy video to demonstrate...
 
https://www.youtube.com/watch?v=4lmK_ILJAfI
 
 

I think you're in a catch-22 situation: if you apply gain when applying effects, then the gain will be re-added afterwards (since gain is at the track level and there may well be other clips on the track); if you apply gain and zero the track gain as part of the apply effects process, other clips on the track will have the wrong gain afterwards; if you don't apply gain, you will - as you say - end up with some effects not being hit with the correct input level.
 
Simple solution...don't use apply effects :-)