You hint at or stumbled upon something known and valid but not really viable. Pathogens having their niches filled with 'neutral' bacteria makes it harder for to spread than just fully sterile. However while real it isn't reliable enough. There is a reason why surgeries involve both wiping down with alcohol before breaking the skin and prescribing a full course of antibioitcs.

So we couldn't do something like 'lets make good bacteria anti-biotic resistant' and chug large amounts of penecilin. In addition to the logistical problems and lack of knowledge for 'approved subsets of bacteria list'. We can't just say dip scalpels in 'neutral bacteria' for internal surgery as a replacement for sterilization. Plus if we were to get bacteria to act beneficially to us that would put them at a competitive disadvantage to their neighbors who don't spend a bunch of energy on playing immune system. But even that is getting ahead of ourselves, to be able to make bacteria behave in ways to reliably replace antibiotics and sterilization would require way more knowledge than we have.