Is there a way to automatically keep a warp train off the ground floor before and after warp transition? If the train is on the ground floor before or during the transition, it will enter manual mode. This requires a manual resetting of the train.

My garden floor spawned in incorrectly and has an extra column of tiles on the left, but holes on the right. Can there be a way to repair / "reset" the garden floor tiles?

Yes there is warp combinator for this reason. You can enable stations only for specific planets

My understanding of the warp combinator may be incomplete, but from my understanding:

1. The warp combinator can prevent the train from entering the ground floor during the warp transition.
2. The warp combinator cannot prevent the case of when the train is on the ground floor and you warp.

Can you force the train away (back to the factory floor) before the warp triggers?

Edit: I am on the latest patch. This is just to prevent the train from entering the "manual" mode and needing to be restarted.

I am looking into this and how to resolve it as it's the most vocal issue right now. It just needs a bit of time to make it well

This is still happening and is quite annoying when i notice science isnt working anymore. If the train is on the ground floor when i hit warp, it goes into manual mode. I do not think i can do anything with ciruits to fix this?

Edit: I can use circuits to keep the train in the factoy level and not come up by using the T from the warp combinator untill a certain amount of time has passed (this will make it not come up during the transition period), but the train will still get borked if you press warp when its on the ground level. So i am remaking my ground floor so it loads super fast and spends as little time on the ground floor as possible.
https://i.imgur.com/CXhbbTV.png

This is still happening and is quite annoying when i notice science isnt working anymore. If the train is on the ground floor when i hit warp, it goes into manual mode. I do not think i can do anything with ciruits to fix this?

Edit: I can use circuits to keep the train in the factoy level and not come up by using the T from the warp combinator untill a certain amount of time has passed (this will make it not come up during the transition period), but the train will still get borked if you press warp when its on the ground level. So i am remaking my ground floor so it loads super fast and spends as little time on the ground floor as possible.
https://i.imgur.com/CXhbbTV.png

If you do not have warp to “temporary space” disabled in your options, then the “T” signal will not be correct. I wrote about it here: https://mods.factorio.com/mod/warptorio-space-age/discussion/6a76e4e89acc92b07674160c
There I also wrote how I solved the problem of stopped trains. Disabled "temporary space". Configured the train to leave the ground station if [T<5] [OR] [other conditions]. And left the factory station if [T>10] [AND] [other conditions]. And now everything is fine. The train can only get stuck at a ground station when warping manually. But this rarely happens. In this case, you must remember to check and start the train. I have an alarm at each station if there is no train for a long time (if the station does not emit the ID of a parked train for a long time).

Fix for this should be comming in 0.4.3