surely you can't simply fly three whites and a red or three reds and a white to fly a three degree approach in an aircraft thats got a different eye height to what the lights are set for.
No, because regardless of what light combination you use/fly, your eyes will always hit the ground in exactly the same place: abeam the PAPI boxes. Flying 3 whites will result in exactly the same touchdown point (length of aeroplane/deck angle/cockpit-wheel height difference notwithstanding) as flying 3 reds. 3 whites is higher than 3°, 3 reds is lower, but you will always end up at the same place on the runway.
Just fly 2w/2r. If you are in a long-body, the PAPI MEHT will/should be set further in so you don't tocuhdown short. If you're in a little tiddler (737, 320) then you will touch down longer than normal (if you haven't changed the aim point to the 300m markers) but who cares, the runway will be more than long enough, unless Aeroscat is doing WIP on the far end!