Harbor Village also has the same timing as Inspiring, Royal Carriage, etc.—i.e., "after" you play an Action—so you can also choose in which order to resolve it and Inspiring. So I guess formally, what this ruling should say is that you may receive the +$1 from the first Harbor Village in that scenario, if you choose to order them properly. Here's how it works:
Play Harbor Village [1].
..Get +1 card and +2 Actions.
..Inspiring triggers: you may play a card you don't have a copy of in play. Decline to do so.
Play Harbor Village [2].
..Get +1 card and +2 Actions.
..Inspiring and Harbor Village [1] both trigger.
....Choose to resolve Inspiring first.
......Play Guildmaster
........Get +$3.
........Harbor Village [2] triggers.
..........Did Guildmaster give you +$? Yes it did. Therefore, Harbor Village [2] gives you +$1.
....Resolve Harbor Village [1] second.
......Did Harbor Village [2] give you +$? Yes it did. Therefore, Harbor Village [1] gives you +$1.
I guess your comment about Royal Carriage has to do with, if you play Harbor Village, Steward for+cards, call Royal Carriage, Steward for +$, then Harbor Village doesn't give you +$ for the second play of Steward? That reason you don't get the +$ there doesn't have anything to do with the timing; you're right that the timing is the same as the Inspiring scenario above. It's because what Harbor Village cares about (apparently) is whether the first act of playing an Action card after it gave you +$, not whether additional acts of playing the same card give +$.
This interpretation of Harbor Village is comparable to that of Conspirator, which says "If you’ve played 3 or more Actions", but actually means 'if you've played Actions three or more times'. This is why Throne Room / Conspirator gives you a cantrip effect from the replaying of Conspirator, even though you've only actually played two Action cards. Similarly, the "it" in Harbor Village's "if it gave you +$" doesn't actually mean 'that Action card', but rather 'that time playing the Action card'.