However I still think your basic premise of a "commando/transport" type fit could well be right. Because I also noticed something else, from DANFS, about the "non-Philippines" boats S-28, S-31 and S-32: all 3 were in overhaul on December 7, 1941. What I'm thinking is that, with the outbreak of war, this capability was clearly (if belatedly) recognized as urgently desired - based on the experience in the Philippines - and accordingly the trunks were installed ASAP on the boats ready-to-hand. And that "commando-ready" dry storage - and/or possibly diver/swimmer lockout - seem highly likely as the function(s) of these trunks.
Furthermore, according to DANFS four of the entire five - all but S-37 - were also sent on to the Aleutians, immediately as available. (The only reason S-37 didn't go, apparently, being that by then she was in really poor material condition.) So, it seems these boats were indeed tapped heavily (percentage-wise), for immediate use - even if they didn't end up doing much, if any, commando-type work in Alaska ( something nobody could have known ahead of time, anyway).
So, I think the evidence tends to support your theory, Donny - I'm certainly willing to buy into it!