I see the free_form_mode.html in the main directory, but I don't see it on the mod list. Is it already installed, and will it be active when I reach the end of the game?

If it's installed it'll appear in the 'Extras' menu.

I've packed both free_form_mode files from the main directory into a zip file and place it in the mods folders, just as the crosshair mod thats already there. Then it is available for selection in the "Extras" menu.

After returning to this game and digging around a bit in the directories, and comparing them to the free form mod itself, it looks as though GOG directly copied the files into the game. What's this mean?

1. Freeform mod is indeed, preinstalled.
2. It won't show up on the mod menu, because it isn't installed as a mod, it's installed as an override.
3. Installing the Freeform mod as a mod probably won't hurt anything.