Once all the brakes, pedals, brake lines, and everything else down there is hooked up, that little area forward of the factory floorboard is probably 50% holes at least. You could fill the other half in with floorboard if you wanted to. There will always be some holes there which you cannot close up, so you'll want some way of keeping small parts which get dropping from rolling into the cracks and jamming your controls.
You'll need to look carefully at how things move and what size to make the holes, so it all fits. You'll also need to consider what all that extra work will accomplish, given there still needs to be a lot of holes. It's mostly an aesthetic choice?
There are some photos of how other builds did it, which look quite tidy.
You would also want to consider how you would disassemble that area if you need to access any give part. You don't want to be pulling controls out too often, it's a big job.
One thing I have learned the hard way, you can never predict what will happen in future and which part of the aircraft you might need access too.
We used the factory floorboards and put marine carpet over top (very light and tough), then I put a small stainless steel wear plate down for the pilot's heels to slide upon. You want that metal wear plate if you have carpet.