I want to use one of the wooden prefab houses but there are no foundations that fit it. Will Bethesda be adding more foundation options and sizes?

How do you mean there are no foundations that fit it? Foundations are just like any other building component, you can snap them together and make larger foundations.

Which prefab? You should just be able to snap the concrete foundations together and drop the prefab on top of them. Same with the wooden foundation.

there is a mod that does that pretty well actually:

http://www.nexusmods.com/fallout4/mods/10140/?%C2%A0

Yeah but then you are left with extra foundation sticking out everywhere. I'm on about different size foundations so you can fit the prefabs on perfectly.

Use shack foundations, 3x3 for the large prefab, and 2x2 for the small.