Starting with jv16 PowerTools 2016, Startup Optimizer has been improved in a way that will allow per-process optimization with custom timer delays as well as processing all of your Startup items using only just one background service that has a low impact on Startup performance. As soon as jv16 PowerTools 2016 will be released as Beta2 (for feedback and testing purposes) later this week, you will be able to test this new functionality and let us know if there are any improvements that we should further consider.
To keep an eye out for jv16 PowerTools 2016 Beta2, feel free to bookmark this thread: https://www.macecraft.com/forum/viewtopic.php?f=10&t=5775