I was able to set CQRLog to type CW with cwdaemon keying the internal keyer of the FT-991A.
The only way I made it work was this:
you plug the USB cable from the rig to the PC you get 2 ports:
/dev/ttyUSB0 that I use for reading frequencies (CAT)
/dev/ttyUSB1 that I set up into cwdaemon by typing into a terminal the following:
sudo cwdaemon -d ttyUSB1
The radio parameter (060) PC KEYING must be set to DTR.
At this point, in the CQRLog, I set CW interface to
CW speed: whatever
Now I launch the CW interface (window; CW type) and the default messages F1, F2...etc are properly keyed but anything I type down with keyboard is keyed twice.
It is probably related to this bug: https://www.cqrlog.com/node/1950
but honestly I was surprised that programmed standard Messages (F1, F2, F3...) are working great.
In fact I pushed the keyer to work at maximum speed you can set into CQRLog which is 99wpm and it works flawlessly.
Well I thought that with exception of the described Bug, this could be used as a sort of guide for those who like to key CW with their FT-991.