Welcome to the board. It's a great resource.

I'll leave your first question about scarfing alone, since I've never scarfed plywood that thin. But I do have a suggestion for your second question about making cleaner cuts. One thing I tried, and it worked pretty well, was to score the cut line with a sharp utility knife before cutting with my saber saw. Any splinters caused by the saw will only lift up as far as the score line, and then they will stop. I never had a problem with splinters on the underside of the plywood because the saw's teeth are pointing up and cut on the upstroke.

I don't know if you have done this, but I cut slightly outside the line with my saber saw and then I use a sharp block plane to plane down to the line. The final edge of the panel is much smoother and more fair than I would be able to do with just my saber saw.

Oh yeah, and I cut two panels at once, one from each side of the boat, so they will be identical.

Hope this helps.