I pretty much sand off all the kit nubs and sand the matching surfaces flat. The older the kit, the worse fit will be, a combination of less precision in the old days and wear in the mold.
I am working with the Hemi from an old Fireball 500 kit and it’s the worst! Once I got the two engine halves together, the front of the engine where the water pump / pulley part goes, literally comes to a point where the halves meet. I had to sand it flat for the front cover part to sit right.
And following along with not relying on kit nubs, I usually drill out everything and insert straight pins for mounting.