Hi,
I had all my rockets set to launch when they're full, so any rocket parts that were still scheduled for arrival would be able to enter while the rocket is launching, and by the time the silo closes again it should take those into account when requesting for the next rocket, the mod wasn't really designed with standby rockets in mind that were fed parts via alternative means.
I am also currently not playing an SE run so all my related mods for it will not be receiving updates (from me) unfortunately.
Glad that you somewhat like this mod though. :)