The other night I did the event “Acquire a skale charmer from Secunda and use it to tag and tame nearby skale” in southeast Plains of Ashford. I was level 17 when I started the event, and finishing the event caused me to level up to 18 – while I was still holding the skale charmer rifle. My second utility skill slot unlocked as it was supposed to, but so did the last one, and the elite slot.
I was able to equip skills in all the slots (using the Mistfire Wolf for the elite), and they persisted after I dropped the skale charmer. They are also still there after quitting the game and logging back in.