I had this. Ended up chasing it down via
– RF turbine cranks, NDS was loose (I didn’t even know it was removable!) and it had trashed the plastic end float thing. Fixed that and loctite’d teh *****. Previously always checked chainring bolts first but this is direct mount and took a while to work it out (i.e. it had to nearly fall off)
Better but not fixed
– As you’ve done, stem bolts, all pivot bolts, took everything out, cleaned off original now very dry threadlock and re-applied.
Still not fixed but suspension now didn’t creak
– Desperation, saddle rails, rear mech hanger, mech, cables.
Nope.
– Rear axle had the tiniest bit of grit on it. Simon Barnes of this parish suggested that. Removed, cleaned, regreased.
Blissful silence ever since. I hope you find it. It took me about 3 week/7 rides and I was ready to set my lovely new bike on fire by the end!