I set a new train down and try to set wait till personal robots inactive and 5 seconds inactive onto stop 1, but when I hover over the train and use the command It doesn't save the stops as the new default wait condition.
When I try to send the same train to a random spot on my rails and it just keeps the default 5 seconds wait time.

I figured out my problem... I had the mod options set to make the train manual rather then switch to the custom wait conditions.
Is there any way to make it do both? If possible I want to make the trains I am manually setting temp stations for switch to manual mode while also applying the custom wait conditions. so I can switch the trains to automatic mode when I am done and they wait for the conditions before returning to their route.
I currently have them set to wait 10 minutes of inactivity but allowing them to sit and wait till I give the manual command would be nice.
Using my personal train for an example, I have it go to a default train stop to refill on some basics so I will call it with the hotkey, do what I need nearby and then use temp stops to send it to the next area I need it nearby, but sometimes I want to send it back to refill so I can keep working without manually picking up a bunch of iron and whatnot, but it 9 times out of 10 leaves a robot behind and I either have to let it try to catch up over the next 10 minutes or manually pick it up, or if i'm working on the outside of my mega base it will fly over biters and get shot down which feels bad.