The primer should cover, As long as its not all chunky in the can, (That can happen if its been frozen). I would sand it flat, reapply,
sand again, using about a 400grit... It kinda looks in those pics that the resin in the mdf is trying to repel the product. It should cover
however. It needs to be flat before you put the vinyl on every little bump will be accenuated,...Btw...Dont sand that coat off, just
knock the high spots down, try not to get back into the wood, It may take a few applications.