When making box joints, per a number of articles I've read, I've left the fingers a touch longer than the thickness of the board. So if I'm making joints on 1/4" plywood, my fingers might be 5/16" long, and then I just sand them down at the end. Some authors (Matthias Wandel as an example) even suggest cutting the fingers with a table saw.
An issue I'm encountering with these is that it becomes difficult to clamp the joint tight, since a clamp ends up pressing on the extension of the fingers sticking out, not the second board you are trying to clamp. I tried clamping a square to inside of the joint, which works well for keeping the joint square, but doesn't seem to apply enough pressure to pull the fingers tightly together.
Is making the fingers a tad longer poor advice, or is there another way to clamp this type of joint? I had considered making a jig with fingers and just a small amount of wood, but with 1/4" plywood, and only 1/16" excess material, it seems unlikely this would stay in place with clamping pressure.