Yes, onlyweapon is the way we attach "natural" weapons (currently hovernets' plasma guns and bloodspiders' monomolecular blades) to characters, they being skipped by the RF code was clearly and oversight, there was no intention to make things harder, the fact that they actually can use RF now is because their weapons had 'reaction' set to true when they were created a while (or in the case of the bloodspider a loooooong time) ago — otherwise it would default to false — so it seems that it was always intended this way...
As for smoke blocking IR googles, the fluff says so, and it was made so — of course "IR vision" is not working as it is supposed to, and I guess it would be even less efficient if it were, but I don't see that happening any time soon.
As for bleeding: yes applies to aliens as well AFAIR, mechanics always apply equally to all teams in this game (and if not that's most likely a bug)
I must say that the game as planned is supposed to be hard as you are supposed to be fighting a losing battle, (of course story aside, game-balance-wise things shouldn't be just impossible, so we'll have to evaluate if planned features are too hard (or just plain unreasonable like the plasma blaster requiring two men and a heavy load cart to even bring out of storage) once implemented, and adjust accordingly) add to that the fact that it would seem like all the features that should make things easier are missing (things like unmanned vehicles for example) and well...