SteamCiv, thank you very much for your report and your input. I´m surprised about the fun this mod triggers on such small maps, as map sizes under 200x200 were not my focus when creating this mod.
The upgrade path will stay for the next biq as this setting saves a precious building slot that otherwise has to be used for separate autoproduced partisans and guerillas. If these units with the enslave option to other partisans/guerillas could be produced normally, they would spoil the game.
Yes, an autoproducing subpen for all civs has good chances to come with the next biq.

The subs will not get the HN-flag, as the sub-bug in my eyes is the "minor evil" compared to free shiphunting by human players on peaceful civs.
I'm just going to have to like my gorillas the way they are then. Perhaps it was the abrupt "no more free workers" from worker houses. If I want more workers, I have to deliberately set aside a city to build them now.
I understand your logic here at last, especially in relation to the building limit. I find it remarkable you have used all 256 buildings and have to use them in the most efficient way possible. In fact, the threads I discovered a few hours ago about the AI and getting them to build artillery (they don't) and the auto-producing building chain along those lines was most enlightening.
Yes there can be some zesty discussion whether hidden nationality for submarines should be on or not:
Hidden Nationality for subs OFF
1--AI nations stumble over each other's subs unleashing war on each other. While they are sorting this out, the human player is not facing the full force of the two belligerents if in conflict with any of them. It might make it difficult for the AI to maintain an alliance against the human player (if that is what they do), because it is conceivable, in executing their attack, they may run over each other's subs, and stop their attack to then declare and execute war on each other.
2--Before sub detecting equipment is available, the human player navy might run over a sub triggering an unwanted war with another nation. By the same token, the human player's sub may not be detected and tripped over by an AI, triggering an unwanted war.
3--the human player can use the sub-bug to advantage. Lay out some submarines near the anticipated path of a nation ship with which war is desired. When that navy runs over it, war is declared without a infamy penalty.
Hidden nationality for subs ON
1-- as described the evil of "free ship-hunting by human players on peaceful civs."
2--nations with subs in the water are constantly sniping friend and foe alike, just like the guerrillas, slavers and others on land.
3--The AI's, while sniping each other's navy on their way to crush the player or other civ, would at least be able to maintain an alliance under those types of conditions (though they may sink each others troop transports loaded with stacks of doom, OOPS)
Solutions?
I agree it can be a big advantage for HN on for the human player. Personally, I can exercise a little discipline garnered from the board game days. I can make my own desirable changes in the editor as needed and then emplace a "house rule" ship-hunting on civs I'm not at war with is CHEATING unless attacking other subs. It seems on land with slavers and lawyers, if you do not get them first, the AI will use HN get you, peace or no . Yes, it seems just like in board games one can create "house rules " for themselves to facilitate certain things as long as it is not too cumbersome.
I experimented with SCOUTS along these lines making them invisible,(trying to find more of a reason to build them early on over something else) that's where I discovered the sub -bug and researched the invisible flags more. One of my scouts died and I was at war with a nation early BC. If I started the AI's with scouts, the same occurred, they were at war immediately in the first few turns because someone ran into a hidden scout. Too bad no one knows where in the hex code to fix that, as I understand in an earlier version of CIV 3, they had the invisible flag work properly.