Well, we could get into a philosophical discussion of why there is even a per-player resources setting, and whatnot.
I'm assuming that dynamix meant it as a "handicap" functionality, where an experienced player vs. a not-so-experienced player could have their resources set lower to "level the playing field," so to speak.
It would make sense though, and as mentioned above I don't think it's intended as a maximum value, (I believe the final output value is a scaled value anyway, keep in mind that morale = condition morale + event morale, and I believe this number is used in the calculation for condition morale). If you look around on the forums there is a discussion somewhere about how morale is calculated, along with commented pieces of code.
I would tend to agree it's not a huge issue anyway (I honestly don't know the answer to the original question about whether it affects morale for a player in a multiplayer game). If it does, this probably goes unnoticed anyway as most multiplayer games are played with morale steady turned on. What we do know is that the resources setting maps to "difficulty" (and the mission code can access this variable easily) so it's most useful as a way to set other mission parameters like how much ore there will be or whatnot.