Tricky one. I know you said you didn’t think it was chain alignment but have you checked it using the following methods? Measure from center line of chain to center line of bike frame at the cranks and again at the rear hub, the measurements should be the same. Or stand behind the bike and look along the chain to see if the rear sprocket is lined up with the front chain ring. If it’s off you can either change spacers/washers (if it has any) on the rear wheel or change spacers (If it has any) on the bottom bracket. Rear wheel option is easier.
However, if the bike just started making this noise it’s doubtful the chain alignment is the problem as that won’t change over time.
Did you lube the chain to eliminate that option as you note in your post?
Have you tried changing the chain tension to eliminate that option? Perhaps less tension?
Sorry I’m not much help.