i think you are overthinking the rationale of your opponents. the simple fact of the matter is that in a heads up situation, 2/3 of the time your opponent will totally miss the flop. therefore, regardless of what you have, if you make a sizable bet on the flop, your opponent will have no choice but to fold. at a low limit table, i guarantee you he is not thinking in terms of chip stack percentages. also i don't think this is at all unique to 6max tables.

1/3 of the time, your opponent will call/raise you with a pair or a draw. at that point, you have to slow down and put him on a hand, especially if you yourself missed the flop. this is where having position on him really matters.

ChezJ