The pros will doubtless have a better insight than I, but my first reaction is that if your drainage pipe is clear and functioning properly, you shouldn't get enough water "leakage" from flushing into it to damage the baseboard over the relatively-short time period that you are talking about. Also, if you are using enough wax, if I understand your description correctly, I don't see why the wax wouldn't just compress into the ridges that you are talking about and provide a sufficient seal. Do you have any specific reason to believe that the leakage is coming through the seal between the toilet and the flange? Could it be coming out from somewhere under the flange (i.e. cracked drain pipe) or above (cracked toilet, as you mention)? Have you tried putting some dye in the bowl and seeing whether it propagates through a bowl crack anywhere?
Sorry I can't be more helpful.
PS Which rivers edge model do you have? There are photos at the manufacturer's web site which you can find with a search engine.