Well I use the qhy9 which is a DSLR size chip and the MPCC keeps it flat edge to edge. it doesn't matter if the light cone is bigger than the MPCC, as long as enough light is getting to the sensor, eg, if your MPCC sucks in say 80% of the 100% light cone you wont loose anything!
As for the Secondary on a 12" F4 if it isn't around the 90mm size you will probably loose out due to vingetting or your illuminated circle will be small hence light drop off will be a issue. My 10" is running a 70mm secondary with approximately 27% Central Obstruction and i have measured with CCD inspector about a 7% light fall off in the corners on the 40d it got to just on 10% so im pretty much using 100% of the 254 mirror's capacity.
If the focuser is anything like the Linear 3" or 2" focuser seen on most GSO scopes... bad news and you will most likely be upgrading very quickly so add a extra 400 bucks to that budget. once again its all good to have a f4 newt, but if it isn't collimated then your off to comet ville! Tube droop kills your collimation/ location of the MPCC! bad joo joos
My 10" has close to 120mm of back focus which is good for a OAG, FW, CCD, MPCC. As for collimation, the only way to do it isn't with a laser it only gets it rough, if you want to do it right Cats eye auto collimator, sight tube and collimated cheshire is the only way to be cirtain that your scope is bang on and preforming well and oh it doesn't have to be cats eye, but a Autocollimator is very advisable! The last thing is the collimating gear on the scope mirror cell and secondary. if its like the skywatcher standards for secondarys...
if they have made them thicker and given them beef then Kudos!
As for flexure... All newts suffer! like Clive has already said you need OAG or SBIG tech to quell the angry mobs! hence what i did! OAG with a 3"FT focuser. the tube doesn't flex that much at all around the focuser due to the secondary vanes that are tight as a guitar string strengthing the circular hollow section!
Sometime soon i will be writing a little novel about my travels and findings for making a cheap newt work like a good quality astrograph.
Brendan