I don't use square knots when stringing because they can capsize and lengthen. They can also slip sideways and one thread will become a Lark's Head knot around the other thread.
I use a double strand and do an overhand knot. With Beader's Secret, I can pull both threads and the overhand knot snugs up tight against the pearl.
When I get to the last 3 pearls, I quit knotting. I drop one of the threads because there's not enough room to go back through the pearls with 4 threads. I take the working thread through the clasp, and then go back through the last two pearls using a beading needle and do an overhand knot with the working thread OVER the passive dropped thread. The I pull both the dropped thread (coming out near the clasp, and the working thread. Then I go through the second pearl, and overhand know over the dropped thread, and pull both threads. Then a dab of glue on those last two knots.