Such benefits for learning have been reported irrespective of when writing by hand using a traditional pen or pencil or using a digital pen (Osugi et al., 2019).
The study you linked does not claim what you say it does. In fact, participants were not even tested on pen and paper writing at all, only digital tablet writing and typing.
Apparently, according to a Japanese study (with an admittedly small sample size), writing on paper beats writing on tablet.
More research is needed, but they suggest writing on paper engages spatial memory in a way a tablet does not.
There are other studies that corroborate this finding from slightly different angles
The study you linked does not claim what you say it does. In fact, participants were not even tested on pen and paper writing at all, only digital tablet writing and typing.