Joe,
Don't worry about it. Just do the "drafting" of the Offset Points onto the plywood as illustrated on Tom Y's webpage. It all works out correctly if you follow the pic.

You need the clearance between the keel stringer's outer bottom edges and the plywood frame to ensure that the skin stays clear of the frames and thus does not "chew" on the skin or cause bumps in the skin which will be not only unsightly but will also marginally slow the craft down for a given paddling effort.

The other reason is probably to avoid weakening the frame cross section by cutting the keelson stringer notch any deeper - see the text below the pic on http://yostwerks.com/SBStringAttachF.html

See also Terry Reed's great blog on his build of a Sea Tour http://dreed.com/boat-building/SeaTour15/seaTour.html
And note the small "blip" he put above the keelson notch to maintain frame strength in this important area A very good idea which I have followed on my Sea Cruiser frame - see the pic below (and note that the commercial foot-pegs have gone back to their owner. My self-made WRC and plywood foot-pegs weigh 160 grams each compared to the commercial ones which weigh 465 grams each)

If all else fails, join the Yost Forum at http://groups.yahoo.com/group/Yost-Skin-On-Frame-Boats/ and ask the great man himself just why the keel stringer ends below the Offset Point - he keeps his eye on posts on that Forum.

Good luck with the build.

Cheers from
Martin Bunny,
Mandurah, Western Australia.
email: mcbunny09@gmail.com