Is there any way you could add an option to only display the indicator sprite in alt-mode? These indicators are super useful but I don't need them on all the time. It seems like this would be a good compromise.
Nope, sorry. The indicators are baked into the sprites for each entity, so you can't remove them without a restart. There is no way to work around it. If you wish to toggle them during gameplay without a restart, you need to use the original mod.