I did not really care about the bedroom count - I was more concerned with basically half of the home converted to a MIL suite, leaving one bed/two bath for the rest of the home, in a market with almost 100% 3bed/2bath. It did force me to find a similar comp - with only duplexes/shared wall units with similar bed/bath counts. Bed and bath count was not the issue - just the work done without permits (not well done); hiding broken windows with a sheet of wood propped up against the window, fencing that was below FHA standards around a pool - just a bunch of stuff that did not meet FHA standards. The bed/bath count was the least of my concern.
I do document non permitted stuff - however I am not the permit police. I will let the lender make the judgement about lending on the property. Lots of non permitted stuff in this semi rural area with ADU's, guest quarters, large cannabis processing shops, etc. When it is common in the area (which is most of the time) I indicate that the "whatever" is not uncommon, the quality of workmanship and the acceptance in the market and if it will impact value and marketability.