Correct - making sure to select the Thermostat Scheduler by app name and not by thermostat.
I am not sure Rule Machine has any awareness of which Thermostat Scheduler instances are restricted, it would have to query the Schedulers (which ones?) to find out. Plus, in theory, nothing currently stops one from having more than one "active" Scheduler for a given thermostat, so this type of selection for Thermostat Scheduler actions remains, in my mind, ambiguous (and to be avoided IMHO).
Consider another workaround: add an action (one per Thermostat Scheduler) to turn EcoMode OFF prior to setting the offset. Does that make the offset setting less "jumpy" ? (works for me).
I summarized the findings in a bug report here and tagged the support team for attention. I don't use EcoMode the way you do but I do use it as well as restrictions so I am exposed to these issues myself.