As you know, you won’t be able to use that to charge 3 cells. Don’t be tempted to try and wire 3 of them with one per cell - even if you use 3 separate USB cables, many USB power supplies are wired in a way which will create a short circuit in that configuration.
For 3 cells in series, you’ll need a BMS (“battery management system”) module (a.k.a. “balancing charger”) with balancing connections to each cell. As you already know, you’ll need a higher voltage power supply for that.
That’s interesting, I didn’t know that. Learned something new today
If the driver is a switch-mode buck driver with reasonable efficiency, then the runtime will be unaffected by whether the cells are in series or in parallel. Part of the prototyping process would obviously include runtime tests to make certain of that.