The "silicone around the floor" thing bothers me. Maybe it's a personal thing, but I've never sealed the toilet to the floor in any of the toilets I've installed. (Full disclosure: I can count them without taking off my socks.) If the seal fails, I want to know about it pronto, and I don't like the look of silicone or caulk around the toilet base.
I'll let others comment on the $400, but I think you got ripped off. As for trying a new toilet, the shape of the toilet, as seen by the casual user, has little to do with how it sets on the flange -- that's pretty standard, in my limited experience. If that many attempts to set it properly have failed, there may be something fundamentally wrong with the waste piping and/or flange. The gob of silicone looks to me like an attempt to conceal a job that was expected to fail.
If you're feeling adventurous, and there's a backup toilet in the house, you could take up the toilet, clean up the mess you're sure to find, and post a picture and detailed description of the flange and its condition, as well as the surrounding floor, and the experts here can probably talk you through a proper job of re-setting the thing yourself. If the flange and/or floor have serious problems (e.g., the flange wobbles around, slots for the bolts no longer can hold the bolts), all bets are off.
-mike