I have a related project that generates patch baselines automatically:
https://bigfix.me/fixlet/details/6132
In this concept, you would stop all previous running patch baselines and auto-generate a new one that contains all relevant patches for Windows in this example. You would similarly generate patch baselines for other categories separately, so you would have multiple patch baselines that would run concurrently.
This hasn’t been done yet, but the baselines could register the need for a reboot at the end of each baseline, and a separate task would actually do the reboot automatically if no user is logged in after a delay, or another would tell the user they need to reboot after a delay. ( In other words, only require a user to reboot their machine if their uptime is greater than X days and only if a reboot is needed )