Section 2, first paragraph. www.ncbi.nlm.nih.gov/pmc/articles/PMC6956183/

At their core phages are viruses, there is no reason to expect the host immune system to not recognize them as foreign and attempt to eradicate them outside the GI tract, where most serious infections occur. The GI tract, skin, and to some extent the lower UG tract will likely tolerate these through mechanisms we tolerate colonizing bacterial flora, but colonization, even with antibiotic resistant organisms, is not a primary indication for empiric treatment for eradication. In fact there are some studies that attempting to sterilize the UG tract in colonized asymptomatic women promote symptomatic UTI.

These colonizations become problematic when growth becomes unchecked and infection develops, or they seed infection into another compartment. There is no reason to think something as foreign as a bacteriophage wouldn’t be recognized as foreign in a sterile space (kidneys for pyelonephritis, liver abscess from migrated gut flora, endocarditis, etc) where these serious infections occur.