What's the theory behind having a bolt on pedal box? Both books refer to it, but I'm struggling to understand what benefit it has. Assuming I can still bolt up the pedals in situ I'm tempted to just weld everything up in the footwell.

Am I making more work for myself?

Up to you really. What I found with welded in floor mount is trying to do anything with the pedals after I'd put the body work on was a royal pain....

My plan for the next time is a top mount bolted on Wilwood affair. Having built a striker with top mounted pedals this is what I prefer for maintenance purposes.

Following on from Coozer's comments, I'd say welding is very permanent and trying to get in the foot wells after the car is bodied is hard work at the best of times. If you have sufficient strength to bolt it in I'd do that to make it easier to remove at a later date if needed.

I welded mine in - if I was doing it again I'd probably have kept it bolted in for access.