Well the toilet is now out......and it's worse than I thought? The lower boards in the first picture slipped around the black plastic (second layer). It turns out the black plastic is the toilet flange - here's the problem. It appears to be a home toilet flange. Even worse, it appears to be cemented/glued into the balck water tank.
I recall reading in the forums that it was originally a screw in flange?
I think I'm now stuck with making this setup work, or removing the black water tank and possibly replacing it. The toilet seals all appear to be in good working order, but with the board rot I'm not completely sure. The damage may have come through other leakage, as I believe the window above, and the trim around the "trunk" were both leaking.
What's the drain tube coming thru the wall and terminating just above the service door? It was ended directly above the raised toilet boards.