My unexpert opinions:
1. No I would not dream of taking off the water trays or even lowering the water level to just a few mm on my VFTs and Sarracenia. The "Inches" rule is a bit wrong because it really depends on how high your pot is. My Sarras water level is nearly at the half level of the pots. 1/4 level is probably the average.
If you don't like mosquito larvae, then just replace full the water every other day.
2. Yes you can use Perlite. Please take note that my Capensis and Spatulatas are now in a mix of LFS, cocopeat and some pumice stones. Pumice stones can also be used instead of perlite, I like pumice because they sink, perlite floats. The idea here is to keep the potting mix from compacting tightly on the roots of your plants, so I don't think river sand is that important. Though I do have and use them too for VFT and Sarracenia
No idea on Nep seeds, I am still yet to see germination on mine
TTFN
Arvin