Another possibility is a spindle or pulley bearing going bad, even though you've made sure it was greased.
The belts can also wear/stretch. Maybe swap just the belts between the decks to see if anything changes.
In the end, if it were me, I wouldn't worry about the noise. If it is a spindle bearing going bad, I would just use it until it (the spindle) breaks. I say that because it's a royal pain to get spindles off, so it's not easy to swap them around for testing purposes.
You've checked everything pretty thoroughly, and there's nothing obvious, so it seems safe to use.
I wear the ear coverings (like headphones) when I mow; that's the best way to fix the noise.....