Have you been on a 745 or 755? The floor layout in no way reduces capacity of these units, and there is a wide connection between vehicles, except for the 755 power unit and the electrical gubbins in the middle of a 745 (and even then there is a large, windowless area where the two half-units are coupled together.
A low floor does compromise capacity, it's a simple fact, the GA FLIRTs however aren't designed to be high capacity units and so it doesn't really impact them.
Lower floors mean narrower bodies (for a given vehicle length), 2+3 seating in a FLIRT would be impossible, whilst being merely uncomfortable in something like an Aventra. The ramps/steps up and down limit what can be done with the seating arrangement, the high floor sections in the FLIRTs have table bays, continued airline seating doesn't look like it'd work above them although granted that is conjecture and would depend on the seating throughout the rest of the unit - it does however make it an awful lot more complicated to fit seats in than if you just have one flat floor. Similarly, the low floor means that you loose vehicle length to accommodate the traction equipment - not so much of an issue in rural Anglia or London-Norwich, but somewhere like the Waterloo Suburban lines where you need all 200m of train to be passenger accommodation or driver's cab it is an issue.
I would also point out that whilst the FLIRTs are walk through, they are by no means 'wide' connections between the vehicles, at floor level they are 'corridor' width - compare that with something like an Aventra which is considerably wider at floor level - you could quite happily stand multiple people in an Aventra or Desiro City gangway, not so in a FLIRT.