And you may well be 100% correct on that...don't know myself...just talking.
My very first MA teacher was kinda "standoffish" about teaching specific applications for his kata techniques---he was worried that if he showed a "offcial" application that people being people we would think that was "THE" application and rather than develop a more flexible set of responses we would "lock in" that it was the "correct" and "only" application.
I think maybe on of the reason that few direct applications were taught is that old timers WANTED people to develop their own applications to the techniques.
Even the Goju I practice where there are specific bunkai etc--what they are really after is effective response to the chaos of a fight...not a slavish replication of an "offical" application.
My own opinion is that such applications were "hugely layered"--but they were INDIVIDUAL rather than stylistic....when I learn a new technique these days I usullay "hang it" on or around something similer I already know and practice.........which is more or less what you just said.
I'm still of the opinion..perhaps wrongly, that many of the old timers of Okinawan katate already had hands on expereince with grappling of some form or the other and simply didn't feel the need to be redundent in their karate training.
My grandfather would sometimes tell me things that he assumed that I already knew part of--such as how to take a viable cutting from a tree/plant---EVERYONE of his generation and region knew this--never occured to him that I wouldn't know how--I mentioned once about a particularly tasty starwberry--he asked me to get him a cutting--assumeing that I knew exactly how to take one, keep it alive, transport it etc.
Sorry to go so far around the barn for an example--but I sometimes wonder if some of the seeming "disconnects" we have with karate etc are due to cultural and period assumptions.
Not so much that were actually "missing" things as much as we differ in our perceptions of what were doing and why.
That the old timers taught us to do "Y" because they assumed that we already kinda knew the preceeding "X" and following "Z" as it were.
Seriously, how long and how often was karate viewed as "weaponless" art when historically it was anything but??
Almost all the old masters were trained with weapons--but many of their students simply had no interest in learning them and for most it simply was not needed anymore.
Wasn't hidden or anything--just many people simply were not interested....so for quite some time the weapon training took a "back seat" so to speak.