DISCUSSIONS on “Rules for online games in HoMM3 and formulas for calculating player rating.”

This isn't clear in the rules; either it needs to be stated explicitly, or it needs to be discussed, because it's unclear why I can't run through a zone if I've cleared a passage to it, even if it's in a different location.

It's actually quite obvious. Doesn't the word specific clearly indicate that the rule applies to a specific passage, and not to all possible passages between adjacent territories?
As for why – that's a completely different question. If there's a passage in another location, then having guards there is a perfectly logical price to pay for passage. Otherwise, there could be a mountain in that location, or simply an impassable obstacle.