I admittedly do not have any experience with Elementary OS, but it sounds like you should be able to add Ubuntu PPAs to it. Is this true? If so, I would recommend installing from our PPA (these instructions would mostly be relevant for your situation -
viewtopic.php?t=2254&p=8461#p8459).
It's most likely simply that you need to add udev rules for U2F and/or patch libccid with the U2F+CCID combination modes.
The package name for the Personalization Tool GUI is yubikey-personalization-gui and the CLI is yubikey-personalization.