Putty does have some flex, plywood on edge is very stiff, and when you point load the hull on a 1/2" wide surface the area around the plywood flexes and the area in contact with the plywood can't move at the same rate.
The putty fills the gap, plus when used as a fillet spreads the load out even further, then flexes at a rated much closer to that of the fiberglass laminate. This makes it less likely to cause cracking.
Some people use putty, other use a flexible adhesive, some use foam, others use nothing, it doesn't make that much of a difference in how you create the gap, or its size, the goal is to just keep the plywood from contacting the hull.