To me, those look like JD Pattern Bellhousings on the engines themselves, then the power unit clutch assembly built from that. SAE bellhousing patterns, IIRC, are all circular, and the JD pattern is a screwed up rectangular-like pattern.
I looked at that pic a bit closer and managed to look at my 3020. That 404 engine set up is the same as on my 3020. The starter is mounted on a flange on the engine and to that, the tranny is bolted (bell on tranny).
Looking at the picture w/ the PTO set up, it is similar to the engine setup on a UV345 International power unit I have. The 345 V8 has it's own bolt pattern, but an adapter was bolted to it to bolt the PTO unit to.
On the picture, the adapter has that mounting pad w/ 4 holes on it. Now, if the adapter is an SAE standard (goes on engine HP if I recall), it might just be easier to mount a transmission to the SAE adapter then trying to make one that bolts up to the Deere engine directly.
A buddy back in the day built adapters to mount an on the road 3208 Cat to a GM Turbo 400 tranny. He was building his own mini semi.... Any how, I hear that at the time, no one else built those adapters, but now (well, back in the early 80's) people started....
If those PTO units are SAE, then it's quite possible there is an adapter out there to mount a non standard transmission to it. Unless you choose something like a 5 speed medium duty truck (ie Clark tranny that was put behind a diesel using SAE housing) and use a divorced transfer case.