One way to help with this issue is to not require the users to reboot right away. Set a deadline of 12 hours and allow them to do the reboot at the end of the day.
It sounds like you are asking how to measure the normal windows boot time, which does not necessarily have to do with BigFix itself.
- Do these machines have SSDs or HDDs?
- Are they on a domain?
There are some tools out there that you can run to measure boot/reboot times. One of them is MaaS360 Boot Analyzer.
You should also be able to look at events in the Windows Event log to see the point at which the machine gets the reboot command and the time it comes back up and measure the difference. This is technically possible to do in relevance, but it is very slow to examine the windows event log and is better done through a task.