Varnishes don't "burn in" and form a single layerless film like shellac or nitrocellulose lacquer, but they do cross-link and form chemical bonds between coats if you apply the next coat while the previous one is fairly early in its curing process. Waterlox is very slow-curing, on the order of months to full cure, which may allow it to cross-link after more than the usual ~24 hrs without sanding. I can't say I've pushed it farther than a day, though: I always do sequential coats of reactive finishes within a day of one another, and less if possible.
The key thing to recognize here is that a cross-linked bond between coats is far stronger than a mechanical bond such as is achieved by sanding. Your scuff-sanding doesn't buy you anything if you apply the next coat while the previous one is still curing, because the chemical bonds that form in that case are stronger than mechanical "interlock" anyway. Furthermore, if you allow the finish to cure before recoating then no amount of sanding can make the bond as strong as it could have been if you'd simply applied the next coat sooner. I would therefore turn your argument around and point out that you're taking the wrong action to fix the delamination issues you've had. The correct solution is to recoat sooner.
Obviously my argument doesn't hold if the sequential coats are of different finishes that don't cross-link. In that case a mechanical bond is the best you can do, and you must sand.