I think you are comparing apples to oranges here. Those SCOREs for the early decks assume play-all through those decks. They are so low because you rarely see the high-advantage counts that you need in order to beat the game. This is why wonging out of these counts is so effective.

However, that does not mean that, when you do see those counts in the first few decks, that you do not have an advantage, nor does it mean that you are over betting. There is a concept called the floating advantage (see BJA3) and it does turn out that your advantage at the same true count does indeed get better the deeper you go. But the difference is so small as not to affect your optimal bet in any practical way.

[edit]
Just saw your comment on unbalanced vs balanced strategies. My remarks apply to balanced strategies. I don't have a lot of experience with unbalanced strategies.