I could have sworn I read this but after reading the RRG terrain stuff I couldn’t find it.

during setup terrain pieces are determined cover 1 cover 2 etc. so a clump of trees on a base plate is determined to proved cover 1.

so if my mini is on or in base plate contact they have cover 1 even if they may not actually have a tree blocking them?

does that affect shooting out of the area?

What you're describing is area terrain, which should be on page 8 or 9.