I would pay little attention to this. You would have to be severely immune compromised indeed, if your body starts to view all your beneficials such as Lactobacillus acidophilus and Bifidobacterium as true antigens. I'd expect that it this point you'd be in hospital in the ICU ward and "under full control" of medical docs, so you would have little choice in your preferred method of treatment anyway.
When it comes to probiotics, I prefer to use and recommend those that are produced by small specialty labs in USA, and preferably not those produced in bulk in a certain eastern country which will remain nameless. Their methods may be OK, but due to a lack of strict quality control I'll stick with brands I prefer and get good results with.
I'd also suspect that if a person gets to the point where their immune system is that compromised (such as in a full blown AIDS patients), then there is little benefit we can expect from any natural medicine in general anyway.