AlgaeFix marine explicitly contains one of these quaternary ammonia compounds as the ingredient, and in my tank it works great at killing algae - shows no noticeable (to me) effect on fish or inverts, and an aquabiomics sample done a month or so after I did several rounds of algaefix reported that my microbiome was "textbook normal".
So, yes. It's totally possible for these compounds to be used as an algacide in a reef tank and kill algae, and not nuke everything.
Regarding pH....
Approximate pH of AlgaeFix marine was ~6.1 and Vibrant was ~6.1-6.2
The dried residues of each was also slightly acidic, not strongly basic. Here's the dried residues with Phenol Red (yellow at pH 6.8 to Red at 8.4, comes out of the bottle red)
L to R: Vibrant, tap water, Algaefix
So the shift to blue color in this test isn't from high pH in the dried drops.