Certainly there are 2 approaches you can take. One is to try to maintain a sanitised environment and then seed your rinds with only the yeasts, molds and bacteria that you want. In many ways, this is what people do when they are making bloomy rinds (although you don't have to try that had because penicillium candidum is an absolute beast and will usually out-compete anything anyway). The other way is to use the yeasts, molds and bacteria in your environment. This is the typical way to make most traditional natural rind cheeses. You might think of it as the difference between making a lager and making a lambic :-)
To be honest, though, there is a reason that most traditional natural rind cheeses are made using natural occurring flora in your environment: it is practically impossible to control anyway. Aging cheese is completely unlike aging beer (I was a home brewer for 20 years before I switch to making cheese -- home brewing is technically illegal in Japan and could affect my immigration status, so I gave it up). With home brewing it is easy to control the environment. You use closed fermenters and basically nothing is going to get in there. I'm going to disagree with you on the need to keep Brettanomyces separated, but obviously you do what works for you. You do a good job of sanitising your equipment and pitching enough yeast and the yeast will out-compete anything. When you are making the cheese, the milk in the vat is similar. You don't have to go crazy trying to keep a sterile environment. The starter culture will dominate and as long as you start with sanitised equipment and are relatively careful, nothing will go wrong (I'm talking on home production scales -- commercial scale is a different issue, just like in brewing).
Aging cheese is more like having a freshly plowed field and expecting to have no weeds growing in it, though. It's just an unreasonable expectation. Like I said, if you seed the cheese with a culture it will have a good head start. Adding geotrichum to your milk will result in geotrichum growing incredibly quickly. But just like seeding a field, there is little you can do to stop "weeds" from volunteering. You need to set up the environment so that it favours what you want to grow, instead. With that, the thing you want will always dominate. There are actually only a handful of things that will grow on a young rind and so you don't even need to seed the rind of the cheese most of the time. If you have the environment right, it will just grow what you want.
Having said that, there are some places you have to be cautious. Mucor (often called "cat fur mold") is probably the most problematic mold. It's prized in some tomme cheeses, but it tends to grow well in bloomy rinds and once it gets established in your cave, it is reportedly almost impossible to keep out of your bloomy rinds. Apparently, before 1970, it was common for Camembert cheeses to have mucor and so you would have this mottled white and grey rind, but sometime after that point, the industry settled on pure white, similar to Brie. French tomme producers often have a separate aging area for mucor covered tommes and their other cheeses and the person who works on the tommes is not allowed into the other cheese areas. I've lately seen a little bit of mucor growing on some of my older cheeses, but for some reason it doesn't like my cave. If I pluck it off, it never grows back again. YMMV.
Gianaclis Caldwell famously advises caution with blues since when she was researching recipes for her book, she had to dispose of some of cheeses from her commercial creamery due to cross contamination with the blue. However, I'm going to say that in this instance, there is a *big* difference between running a commercial creamery with hundreds/thousands of cheeses and having a cheese fridge with a few cheeses. Especially if you are using maturation boxes for your blues, it's not hard at all to contain the blue. To be honest, if you can't do that, then you probably can't maintain natural rinds in good condition at all. It takes experience to get good at it.
The thing about doing commercial affinage is that you have hundreds/thousands of cheeses all doing the same thing. So the commercial cheese producer has to do almost nothing other than to keep the humidity at a decent level and turn/brush their cheeses every day. The cave takes care of the rest. So it's a much bigger problem if your cave decides that you are making blues now :-). At home, you just change your environment, baby the cheeses and everything is fine. It's just not a thing you can do at scale, though.
So anyway, every situation is different. Everybody's cave is different and everybody has a slightly different technique. You'll find your stride over time. I find that affinage is at least as deep a topic as making the cheese in the first place and there is a *lot* to learn. I don't believe you can control it the way that you control fermentation in brewing, though. Maybe if you introduce everything yourself, keep everything in maturation boxes, wipe down all your surfaces every day, etc, etc, etc. But... I don't think that's necessary or even desirable. YMMV.
