I think you might be on to something ;-)
I think it would be very difficult to stove a conventional landing craft made of wood or metal in any collapsible form.
So maybe it is correct the way the Aoshimakit is showing the cargospace in the rear as just a hole, which could be planked over, and have the "RIBs" stowed in there. and then just attatch the two landing crafts on the deck, using ropes or something.
Anyway i find it is very strange, that almost no information is available of this D type/ Landing craft project.
I mean this is a quite unique project.
also the whole transport-submarine is quite unique.
And even if it looks like a dead-end in submarinedevelopment, one should think it would
get more attention, - just my thought

In this link I previously posted about the subs:

http://www.navypedia.org/ships/japan/jap_ss_d1.htm

Under the heading of "Military load," it says:

"2 13m Chuhatsu or 14m Daihatsu landing craft, 2 RIBs, 110 troops, 82t of cargo"

So, first of all, it lists either Chuhatsu or Daihatsu landing craft. But, it also lists "2 RIBs." RIB (or RHIB) is a modern craft, not WWII. It is a Rigid Inflatable Boat (or Rigid Hulled Inflatable Boat.)

So, it occurs to me that this might be referring (with alternate terminology) to the collapsible boats you have read about. It seems possible that--in addition to depth-proofed standard landing craft--these subs also carried a couple of some sort of "inflatable," or "collapsible," or "stowable" type of boat as well.

You said the translation was a bit garbled. Perhaps it is trying to indicate 2 different types of landing craft--one large/substantial and the other small/stowable?

Just a thought.