Here is the item again:
If his friends walked into the bookstore
(A) Boris had a stack of car
magazines as camouflage, (B)
but he was really reading Better Homes and Gardens, studying
decorating ideas (C)
to spruce up his first apartment.
You correctly realized that a comma must follow bookstore. If his friends walked into ... is a subordinate clause. When a subordinate clause introduces a main clause, you connect the two with a comma.
To fix the problem, you chose to do this:
If his friends walked into the bookstore, Boris
had a stack of car magazines as camouflage, but he was really reading
Better Homes and Gardens, studying decorating ideas to spruce up
his first apartment.
You have correctly employed Punctuation Rule 2:
Subordinate clause + , + main clause.
Excellent choice!