If retaining the stock style suspension I would leave it open to allow the needed access for alignment. Fabricate panels that snap or bolt in and paint them body color. Not as clean but...
If suspension mods eliminate needing this access for assembly and adjustments you can fill them.
Seems like a lot of work for relatively non visual areas. Easy to see with empty bay. Now add motor, starter, exhaust, brake setup, possible clutch, etc...
My2c