I received a Fukien Tea as a gift. In hopes of discovering some interesting roots to develop nebari I dug it out of the pot to find about 2-3 inches of the trunk buried with a fist size rootball at the bottom of the (deep) pot. Unfortunately I found only fine feeder roots so I repotted as received.

I’m not familiar with this species but I know generally potting too deeply is not healthy for the plant. Is this okay to do with a Fukien Tea?

Fukien tea trees are not ok with anything. It seems like if you are in the northern hemisphere, no matter what you do they die. You Messing with the roots might have an effect on how long it takes to the unavoidable.