On the Bootlegger mod I built for the wife, I've had her charging the 18650's via USB overnight because it lasts her the whole day under normal vaping. But if she forgets to hook it up or happens to vape more than normal, the batteries are easily swapped out. And I did up the cutoff to 3.2v as well. I kept an eye on it the first night and it charges the 18650's same as the lipo... tapers and stops at max capacity, 4.20v for each cell. She's also vaped while the USB is plugged in without any issues.
I'm not worried about the USB port... it's not like Evolv said they'd only warranty the USB port for 3 months like another company did. If a person uses common sense and doesn't stress the port, I feel confident it'll be fine. I've charged and vaped while charging the Opus, Boxer, and Bootlegger and they all feel solid at the port. Now, if it was someone like, oh lets say my daughter, who has ruined the USB port in every phone she's had because she trips over it while plugged in, yanks the cord out by pulling from about a foot away from the port, and even dangles the phone by the USB cord while plugged in, then yes, that person should definitely stick with charging the batteries via charger! That's not the fault of the device though.