Yes, I agree with you, ct1 is just ignored and ct2 is applied with all of its settings/mappings/aliases.
Legacy index template has the order-and-merge behavior, which is useful to avoiding wrong field mappings(the problem for this topic). but as its name indicates, I feel like it's a recommended option for us since it's a legacy feature and might be discontinued someday.
So we're circling back, setting auto_create_index as a whitelist is a valid options to solve the problem we're facing.
Actually there is already another topic going on What is .ent-search-*-logs-*,-.ent-search-*? where is it from?
I've been so happy discussing this topic with you by which we've made a good understanding about index templates. You're so helpful.