I’m assuming they meant that they were company phones, and that additionally they were required for any work related MFA requirements.
If that’s the case, it would be YubiKey in addition to, not instead of.
As for the time tracking software, those are often part of a much larger accounting, payroll, and/or HR software suite. Having his team spin up Windows vms, or even have separate older windows boxes somewhere, probably makes more financial sense than not. At least, until they can switch to a more modern suite that has a web portal.