I think the only real registration problem with having a full weld in cage like this is the side intrusion in relation to ingress and egress ADR's. You could make the side intrusion a bolt in piece and remove it when driving on the road.
If you remove the back seats you need to re-register the car as a 2 seater - i.e. go over the pits.
Brown davis have photos of one they have done (think Racepace look after the car - grey R32 GTR) - full weld in cage, then the rear seats stuffed in behind the bars, and Vicroads is happy with it - this car is completely road registered as a four seater - you just cant sit in the back!
Another consideration is compliance with seat mounting - you can have an ADR approved seat (like the Velo GPT-2 - my passenger seat), but not sure about mountings - if you can retain the factory mount as well, then you could just drop your standard seat back in while driving on the road.
With regards to interior - you really want that roof lining out if you are taller (I am 6'2'') so the bars can run as high as possible. Once you have a helmet on, and you have padding on the top bars, you are likely to be resting on the padding. Otherwise its really just a matter of convenience - getting to trim panels with bars in the way is likely doable albeit hard, you might wreck them in the process I guess.