I thought I'd ask all of the members who have built themselves MDF flooring in their boot what the benefits of doing so are. I'm planning on constructing one of these for myself while my car is in the shop for the next few days.

I have a second gen, and I took a gander at the interior of the boot, and the chassis seems rather uneven, which leads me to my next question, how will I mount the floor to the chassis without drilling into the fuel tank, and how do I deal with uneven flooring (spacers perhaps?)

I rebuilt my amp rack so it sits right under the ski port now, so I'll be looking to mount that straight on to the flooring. I'm also planning on sourcing some slimmer subwoofer boxes, so I can mount those behind the wheel arches toward the back of the car so it won't interfere with the spare tyre door I'll be installing.

Any advice would be greatly appreciated.

If you make the MDF a tight fit, you shouldn't need to mount it to the floor as the walls of the boot will keep it in place. Once you've mounted the amps and subs to the floor, it should keep it in place for bumps etc.
I think the biggest benefits of an MDF floor would be the fact that you can mount stuff to the floor without having to drill into the chasis, and you can create a door for your spare tyre.

I agree with M4DDOG except would suggest plywood rather than MDF. It won't fall apart if it gets wet, unlike MDF or masonite, especially if painted or varnished. Of course it shouldn't get wet in the boot but accidents happen. Plywood is much stronger too. At least 8mm thick or more should be adequate. Try to get it from somewhere like Mr Ply and Wood rather than Bunnings. You should get better quality for lower price.

I completely replaced the masonite in my TP station wagon with plywood and it made an enormous difference. You can crawl all over it when loading without worrying about putting your knees through it and can carry heavy loads with no fear of it collapsing. I also did the boot of my previous TM sedan and am about to do my current TP sedan. Wouldn't be without it!

Plus plywood is so much lighter than MDF.