Very engaging hypothesis there, Don! And easy enough to investigate - at least a little bit further - by looking at the DANFS histories of these 5 boats. Of the three clearly having the "full trunk", S-37 and S-41 were indeed very active in the Philippines - actually, with the Asian Squadron for (at least) the entire decade prior to WWII. But the third one, S-28, had not been based further west than Pearl Harbor and then returned to San Diego to teach Underwater Sound Training School. Meantime, the remaining two - S-31 and S-32; the ones appearing to have had "mini-trunk"s - only operated, in the decade leading up to WWII, between New London, the Panama Canal and/or Bermuda. So, the feature couldn't have been strictly a "Philippino mod".

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!

Cheers,

-Matty