If you go with a "natural rind," then yes, mold is inevitable. In that case, the idea is to let the mold develop, but brush it down periodically to keep it from getting too wild. After a time it will consume all of the food at the surface, and stop growing. This WILL add flavors to your cheese, flavors which will not necessarily be limited to (though will be strongest at) the rind. I don't know the exact mechanism, but just as salt works its way through the cheese, the flavor (or enzymes, maybe?) seem to make their way through as well, though not nearly as quickly.
If you go with a b. Linens rind, you are actually encouraging a reddish bacteria to take over, and it will out-compete the molds. Again, it will add flavor(s) to the cheese, again not necessarily limited to the rind.
If you vacuum seal or wax, in theory you will deprive any mold of oxygen, thus keeping it from growing. If you wax hot enough, the heat may also help to kill off mold on the surface. However, keep in mind that blue mold in particular is extremely aggressive, and can tolerate low-oxygen environments, so you may get some growth under the wax/plastic.
If you are getting a blue mold, that will probably be obvious. If a whitish mold, that is likely geotrichium. (Could be PC, but I don't find that that grows without specific encouragement - YMMV.) If you get other colors - reds, yellows, etc. - you have the "natural flora" at work. My understanding is that none of them will be dangerous - ?? - but some may lead to objectionable flavor.