Ya I tend to agree. Any more than about 65% of Thread engagement gives very little additional thread strength (pull out). If % of thread is the goal you'll simply be buying more taps and dies than needed. As you said shear loads are not good on the threaded portion of a screw.I'm not convinced a tight fitting screw is a good thing. Any idiot can tap a hole that will fit a screw tightly, but that is not how a screw is meant to work. Screws are very good at resolving axial force (i.e. the screw works in tension) and very bad at resolving side and bending forces.
But, if it gives you the 'warm and fuzzies', go ahead and believe it.
dld
Layoni's design is interesting. I assume he got the idea from standard Morse taper tooling. Very strong and accurate design. In fact he said the original design didn't have the threaded pin but sometimes it didn't hold but more often you couldn't get it apart.
IMO the best joint is the wood pin into wood particularly if you're looking for a tight fit. Two advantages other than 100% wood. 1) The pin is cut where the threads stop approx 3/4" before the flat face. This adds shear strength much like a Shoulder Bolt which is made for this purpose. 2) The unthreaded portion can be custom fitted Exactly how you like it. One way is to add coats of super glue, sand, coat, sand..... to perfection.