The act of bunny proofing your home is about providing a safe and comfortable place for your rabbit(s) to play and exercise while protecting them and your home from incidental damage from the rabbit's natural tendencies and needs (e.g. chewing). The practicality of doing this to your entire home depends, of course, on your home and that's where the caveats/considerations come in:
It's very difficult to ensure that you protect everything. For the most part, if you're okay with a bit of chewing on some wood furniture or such, then no big deal. Electrical, however, is where it gets a bit scary. You might miss something (easy enough to do in a larger space) or the rabbit might eventually chew their way through the defence. Regular inspection helps, obviously.
Stairs and other high surfaces in the home can present a challenge, but not an insurmountable one. I agree with her general assessment (in the linked article), all of my rabbits liked to get up on things (especially after being brought up to them once), despite people trying to tell me that, as prey animals, they would avoid that. It's anecdotal, but I've seen a lot of such anecdotes... My concern in this environment is risk of injury from falls or miscues with more slippery surfaces. Rabbits, in my experiences, have a hard time with slippery surfaces and while they tend to have powerful muscles, their bone strength is not as good, and so I would have some care about where they might leap and slip and cause injury.
My general feeling, at least, is that having a large, but more confined space may be better and easier to do as it's also easier to supervise your rabbit(s) in that environment. Having said that, if you take some precautions and inspect your proofing efforts on a regular basis and repair any showing signs of being breeched, then I think you can allow them to roam freely. That is, after all, the best way to interact with them and, I think, keep them healthy and active.
(I never could give mine free run, my house was just not practical for it, so I set up a huge space in the basement for them (about 100 sq feet), which was shared with my home office and so allowed for me to be with them very frequently and interact while giving them plenty of space to do the bunny 500 at will.)