When you pull the carpet out, there will be a small gap around pretty much anywhere the plastic parts meet where the carpet was. The center console is probably the most noticeable. However, assuming the plastic mounting holes inside the console haven't broken yet, (They often do, if you get people on either side leaning on it in winter when the plastic is brittle, or making out in the front seat) it is still pretty rigid.
The other area you will notice the gap is the trim around the bottom of the doors. If any of that bothers you, you can track down some of that clip on weatherstripping and run a strip of that around the bottom of the console before you reinstall it.
Assuming that you don't break any of the mounting points, there shouldn't be any new rattles once you pull the carpet. At least not in my case. I did notice it getting a fair bit warmer without it, but once i added the bedliner, it became completely comfortable again. It still added heat, but not enough that it couldn't be overcome by turning the vents a little colder, or opening a window. It actually helps a fair bit in winter. At least on the passenger side, since that is where the exhaust runs. I didn't notice it getting any COLDER in winter either, but most of my heat loss is because I removed the plastic door liner, and didn't replace it.
I did do my cargo area as well, in addition to underneath the rear seats. Not sure if that was a good idea, because cargo likes to slide around now. Once I get a rubber mat, it should be okay. The biggest worry for me though, is the wires from underneath the console. Now they are exposed to trampling feet. But, like what was said earlier, some wire looming and zip ties should make that a non issue. Hopefully.