I really like this game system, it was the first in a family that included SPI Wilderness Campaign (which also included the Overland Campaign) and Lee Moves North (for the 1862 and 1863 invasions).
I do not think Forts are inverted in the Standard Game as they are not combat units. In any case, their hex and value is noted in the set up and they cannot move, so hiding them seems to have little purpose. One can of course put a combat unit or a dummy in a fort; the latter is one of the better uses of a dummy counter, I think.
I made some derived errata for this game to clarify some areas of possible ambiguity.