Yes a one piece trunk floor can be installed with the 1/4's still on.I have done it.On a Charger,it can be done by removing the rear valance panel[which a Charger usually needs anyway],and removing the tailpanel which is actually easy on a Charger since it is welded on top of the 1/4's ends not under like other cars.

I have installed the repro outer wheelhouses several times on B bodies.They are a real dissapointment.They look great until you try to fit them and they are way off.
They fit much better if you leave the original pinchweld intact at the outer/inner wheelwell seam and splice the new outer about 1/2 inch on the outside of the pinchweld.That way you can adjust the position and don't disturb the original inner to outer pinchweld which is a continuous resistance weld.Plug welding the repro outer to the original inner opens up leakage issues.From what I have seen,AMD's panels all look way better than Goodmarks.