Per the suggestion of several people here, when we bought our toilet we inspected it. However, the store did not seem to have any available floor personnel or any obvious way to do this prior to purchase.
So we simply bought it and took it outside, then opened the box in the parking lot. This took only a few minutes. Had anything been wrong, we could have wheeled it right back in.
In the end everything checked out and we were fine with the first unit selected. I would point out, though, that the first box we pulled had clearly been dropped, so we went a bit further back in the pile to get one that looked unmolested.
If you're at one of those stores that's not very helpful, you still have the option to inspect before taking it home. Plus, when you have a time stamp on the receipt that shows only a few minutes have gone by, it's pretty clear you didn't bung something up during installation.