I placed some Stained Glass Doors on trains and set them on 'Manual mode' with the Wrench. I expected them to not open when the train aproached a station but they did as opposed to Create's Framed Glass Doors witch only open in 'Manual mode' when R-clicked.

I used Minecraft 1.20.1 with Create 0.5.1j and Create: Framed 1.5.5

which modloader are you playing on?

I am using Forge 47.3.6.

Hey, so reading back through the original comment and also doing some testing, I'm not entirely sure what your issue is. I can't seem to use a wrench to configure framed doors of any variety, only through the train station. Of which the "keep doors closed" option seems to work just fine.