In your plans you show covering the inside of the control box with a piece of fiberglass cut on the bias. I tried this and couldn't ever get the corners to stay put.

It is a little tricky. It is easier with lighter glass. It doesn't need to be perfect, even if you cut out messy corners later this does more than no glass at all.

I'd think it would be safe to leave this unglassed, much the same as the skeg knob and handles are epoxied/varnished but not glassed. Seems like glass/epoxy is more for strength and abrasion resistance.

It is probably OK to leave it unglassed, but as a general principle I like everything under glass just for long term protection.

I'm also toying with the idea of trying Etienne's method of glassing the inside of the deck first, installing Maroske fittings and the skeg control box, and then glassing the outside of the hull.

I think Et's system is a good one, no reason it shouldn't work for you.