Maybe the supply could be used independently for naval and land -- the balance between the two was the crux of the reasoning to make the naval buildings give supply in the first place iirc, so let's just silo them completely
So say you have 10 supply, you can build 10 land AND 10 naval. If you build 11 land and 11 naval you're same as 2 units over as far as current penalties go, but otherwise each counter works independently