I've ended up with imbalanced bets once in a while, usually if I'm really trying for cover, sometimes if I'm drunk:
a) It's somewhat more difficult to ensure that you have the same aggregate bet out there. If you try to make it look like you're working a "system", it's even more complicated.
b) In the long run, it shouldn't matter, but short run I think it might increase your variance a bit, if you get unlucky or lucky with the bigger bets.
c) It's actually kind of fun when you feel like you're playing like a crackhead.
And I've seen ploppies playing independent hands. Most remarkable was a guy using a positive progression system on two spots. If the spot won, he'd add a green chip, if the spot lost, he'd revert to a single green. I happened to catch the streak when the second spot had been on a wicked winning streak, and had a very large stack of greens on the spot. Maybe $400. The first spot kept losing and getting replaced by a single spot, and the monster spot kept winning. It was quite a sight (he said he had been playing all weekend for that to happen).