In many apps we are putting the sync of the MxModelReflection in the after startup, so the configuration is always setup correctly. The problem is that until the application is completely started, end users must wait to be able to access the app. On top of that: The app fails to start when the after startup is taking longer than five minutes (currently experiencing this).
My suggestion is:
After startup microflow shorter logic.
Delayed after startup for longer logic, such as MxModelReflection or auto setting configurations.
De delayed after startup must immediatly be triggered once the appl is running.
You could use the Process Queue module to achieve what you want I think.