You put it better than I.
The psychological conflict, I think, is that one may view somebody's "code" as a sacrosanct expression of their personality. However, this is rather a work of putting many things together and building a machine than putting them side by side and making a gallery; a badly thought out part is not just like a part you might not like, it affects everything else. I would rather advocate the simple view that your code is only meaningful if it's fun to play. Therefore, any well-meant improvements should be, by default and so assumed, welcome (unless we completely missed the point of what you were trying to do).
I mean, who cares if you made something that's very cool but breaks the game? The universe is littered with pointless mods. If nobody wants to play it, it's irrelevant and it doesn't express or deliver anything to anyone. And on the contrary it's relevant if it makes people happy. Therefore, players come first. Therefore, bug and balance fixes, keeping players happy and constructive criticism come first, politics and keeping modders happy later.
That's how it must be to work efficiently... on the other hand, to paraphrase someone, who should care if the cat is a punk rocker with a safety pin in his nose so long as he catches mice. This is not principle, it's just an attempt to make things work.
In bug news, this:
[USE_MATERIAL_TEMPLATE:RAW_APPLE_TREE:PLANT_STRUCTURE_HLG]
[STATE_NAME:ALL_SOLID:apple tree] <--
[STATE_ADJ:ALL_SOLID:apple tree] <--
causes you to find "apple tree bolts" in adventurer mode. Suggest change to "apple tree wood" or "apple wood" in marked lines.
@Lost in Nowhere: you would want the creature to shoot jets of fire, perhaps? Material emission is your friend. The vanilla version is included in this mod because it's so near "hard coded"; see the wiki syndrome page for usage.