I don't see any problem.
The inside of the head tube doesn't have to be smooth. The bearing cups should be smooth. If the headset bearing is to tighten, you can sand down a little bit of the horizontal part, not the slanted side.
When the seat tube isn't smooth, that's also not a problem. Especially when the seat post can slide in. The part that should be smooth is the inside of the seat tube where the clamp is placed. Only this part will hold you seat post on place en should made good contact (in combination of carbon paste).
So, I shouldn't worry to much. Build up your bike and have fun....