When there is something like a Servicing Stack Update in the patches, MS says that it needs to be installed separately from all other patches and requires its own reboot. In those cases, I am putting in a separate fixlet to reboot the endpoint before moving to the rest of the patches in the baseline. I’ve found if I don’t do that, then the endpoint tries to install everything, does the reboot at the end of the action, and then has to retry installing most of them again. In fact, it often requires 3 total reboots. I don’t honestly know if this really make a difference for the overall amount of time required, though.
To be honest, many companies I’ve been at have found that they run into problems with patching if they don’t reboot every endpoint right at the start of the patching–no matter which patching tool they use.