point by point...
If you want to save money with this guy or do it yourself, it is a risk. But here's a breakdown of these issues.
1) Wax ring not going on right: I guess it could happen. If so, toilet will leak out of the bottom. If you have tile, you're probably okay. The floor should be covered with plywood, and then a "watertight" layer like cement board, then mortar, then tiles, then tile grout, then tile sealer. The floor is made to get wet and protected. I guess all hell could break loose, but it's unlikely in my amateur opinion. To fix this problem you just scrape off the old wax ring (it's soft wax, especially when new) and press on a new one. It's easy and most plumbing books have great pictures for how to do this.
2) The toilet becomes loose and starts rocking / leaking: Get out a wrench and carefully retighten the flange bolts. Pack them with plumbers putty, too. Or use plastic shims. These are all very easy fixes and they can happen even with a great plumber who probably won't shoot out of bed our duck out of a big job to put a plastic shim under your toilet.
3) Tank to bowl connection starts leaking: There's again a bolt there with a gasket. Just tighten it carefully. Don't overtighten it or you'll crack the porcelain.
4) Flange bolt cracks the bowl: This probably the most likely of the problems. Just watch the guy and if you hear a crack when he tightens the bolts, say, "what was that? Did you just crack the toilet by overtightening a bolt?"
5) Supply stop starts leaking: I assume this is because the "plumber" somehow wacked it. Again, watch him do the work. If it leaks, it can be replaced fairly easily. Ask the guy who does it to check it for leaks before he leaves. Check it yourself. Wipe it dry and then run a paper towel over it to check for leaks.
Hey, I'm just a homeowner who does occassional plumbing on his own house. So make your decision however you want. There are benefits to hiring a pro at $150 a toilet and benefits to saving money on something that is probably an easy job for anyone with a little plumbing experience UNLESS YOU ALREADY HAVE A PROBLEM with the toilet or shower.
Good luck with your choice.