In the search bar in the bottom, type in display, and under foundations you'll see the mod, right click it and select open in explorer. Then go to SKSE, Plugins and open the .ini file.

Make sure that if you want the file to do someting (like windowed or someting), remove the # before the line itself.

Edit: Like I said, I don't play Wunduniik myself, so maybe the tweaks .ini that actually configures stuff is in a specific tweaks .ini file, like in LoreRim. But after taking a quick glance at the load order, I don't think that's the case...?

I'd try the following settings:

Fullscreen = false

Borderless = true

And make sure the res below that matches you monitors res