I have had it confirmed by the supplier that the pumps dont have to be above the toilet rim as the manual suggests. This is only true to prevent siphon back but I have already made a siphon safe system via my pump up gravity out tank system. So with that resolved I can continue with my planned install.
The toilet base that I glassed in is set, so I cleaned it up (ground and sanded sharp edges) and positioned the toilet on the base in its correct position (centered left to right and the correct distance from the front edge and the lid hinges square to the centerline) and marked and drilled the 4 mounting holes. I bolted it down so that it could not move, pulled down my shorts (they are glue encrusted) and gave it a test sit on. Comfy! Funnily enough I have spent quite some time sitting on that imaginary toilet contemplating my next move when designing the ensuite furniture. Anyway, next step was to position the pumps (manual must be to the bulkhead as it is pumped through the bulkhead, and electric must be first in line) so as to be sure I could get them in and out without having to remove the toilet. It all fits and works out. I can move each or all of them independently of the others and can get to each without much trouble via the top. The pumps are also supposed to be no more than 45 degrees off vertical and this is also no problem.
I then made a cardboard template of the top with the toilet cut out of it. I will attempt to have a top that sits tightly against the ceramic bowl sides and will line that with a white rubber seal to close off the gap between the toilet and top edge and only some white capped screws to hold the lid down in the corners visible. That way the lid will conceal all of the workings of the toilet leaving just the lids. A nice clean white look hopefully and easy to keep clean.