Best option is to choose a design that doesn't really need a skeg . . . and there are plenty.

But, your idea will work fine. It's just like building a daggerboard trunk in a SOF sail boat. I build the frame, complete with trunk and slot for the board, skin the boat, then cut the skin for the slot. Then I squeeze in a lot of construction adhesive, or 3m 5200, and staple down the skin. Works great. Your aluminum plate will likely work just as you say.

Good luck!