Can I enter License Key/License Server URL via Command Line when installing ReSharper?

No. License Settings management cannot be done via the command line now, so it should be configured manually on users PC after installation completes - on the 1st Visual Studio (with ReSharper) launch, or later in the ReSharper | Help | License Information dialog.

This is a common request, and we are considering adding some "command line" commands in the future for these kinds of needs.