Either approach has benefits. Squat stands, made or bought, can be moved out of the way into a corner so they're very handy if space is at a premium, and can be cheap to make. I like a 4x4, measured to just above your normal rack height and then cut a V into the top. Fill a 5 gallon bucket with cement, center the pole in each of them and let it solidify.
The other approach is good too. I've written about good things bottoms up squats did for me in other threads, got some disagreement about it, but it's an ok thing. I think it's a good thing to train this way for a while personally. I personally didn't have any trouble with my top numbers, although they weren't at their peak when I went through that phase. It builds starting strength, and it's much easier to train an SSC rebound out of the hole than it is to train actual starting STRENGTH out of the hole. So maybe they take a dip for a short time when you finally get back to the real thing, but it's going to come back real quick a) because you're actually stronger in the position and hence can get more speed out of it and b) because training a rebound effect is much quicker and easier than straight strength, and c) your back will be stronger from having to muscle things up, at least that's the effect I've noticed.
The other thing is if you take that approach it is a great time to really focus HARD on mobility and flexibility---you are using less poundages anyway, so no fear of losing more, and it will actually help you get stronger because you'll be able to get a better set-up to start in the bottom with the extra mobility (mobility tends to make you stronger anyways because you're healthy, but that's a very unsexy way of thinking for most of us).
Also starting in the bottom is a skill just like anything else, so it can be more "comfortable"/stable just through practicing said skill. For instance, the first bottoms-up front squat workout I did this year was terrible...something like 80% of my 1RM regular front squat as my 1RM from the bottom. 2 weeks later it had jumped up by 10%. That's easily enough to get a training effect either way--especially considering there's no stretch so you're actually working the muscles HARDER in the hole even though the weight is lighter (see Thibaudeau's thoughts on the matter), plus more stabilization, so you don't need to be hitting the same numbers you were in the first place.
So really, it can be done either way, 4x4 wood is cheap and so are paint buckets and cement.