I've released v0.12.1 for factorio-1.1 which should hopefully sort this.
There's a new mod setting to override the vanilla temporary stop wait conditions, it will catch the event and replace the 5s wait condition with 'Passenger Not Present'. It'll also detect if a second temporary stop is added after the current one and it'll then drop the current temporary stop from the schedule. When I was playing around it felt nicer that selecting a new temporary destination automatically forced the train to go straight there.
The boarding timeout setting also now allows a value of zero which will then use 'Passenger Present' as its wait condition. Any resulting carnage on your train network is on you ;-)
If you need a backport to 1.0 let me know, though it may not be today