I don't know if this is your problem, but when my bikes sit for a while, the rotors get a bit of corrosion (not really visible). I will have a bit more dragging noise when first riding after sitting (or spinning them up on the lift), but it soon disappears with running and brake use.
Also, when I really clean my bike, I scrub the brakes, rotors and all with smaller stiff bristle brushes and a mild corrosive like S100 or auto parts mag wheel cleaner, followed by good rinse and leaf blower dry. (For more intense cleaning, I use gun bore solvent and a pistol rod with old beater brass brushes on brakes and pistons)
The brakes are always smoother and quieter after.
My rotors have never been changed (60K and 107K) and are definitely worn with an outer lip, and may even be out of minimum speck, but all cleaned up they still work great.
The danger with letting them get too thin is cracking. Especially on a mountain road where they may get hot. Saving a few $$ is not worth it. If they are below minimum spec replace them. Friends don’t let friends ride on worn brakes.