Roll20 doesn't perfectly match the LoS rules for a bunch of systems, as a result of allowing all of those systems to be played on the same VTT. Honestly, the LoS/Spell effect rules are a bit garbage in a bunch of game systems anyway - I'd highly recommend finding a ruling system that works best for you and your players on Roll20 and making those rules explicit and consistent for your players. This might mean making one large DM ruling for your PF games "THIS is how we do Line of Sight, because Roll20" ... but that will save you from making constant, small DM rulings on the same issue. There's also that constant of DM rulings: the same rules apply to the NPCs. As long as it's consistent and explicitly stated, no one is disadvantaged. It's not a perfect system, but leveraging DL and LoS to work for you makes it much more immersive for the players - it will require some tweaking of the rules, regardless of the system. Just be consistent, and let hardcore 3.5/PF players know upfront about how LoS works on Roll20 and that you've adjusted the rules accordingly.