In effort to limit the number of layers created on the map to those specific to the SIEM App, a layer is only created for values in siem:defaultIndex that have a Kibana Index Pattern that is an exact string match.
While this ensures the map is created with only relevant layers (ensuring both performance and data relevancy), it has caused some confusion as to how and when data shows up on the map. We've improved this by adding targeting documentation, updated inline messaging when no matching index is found, and further details in the maps documentation.
I think one of the last remaining things we can do to streamline this UX is to enable pattern matching when determining which Kibana Index Patterns are relevant. This would mean that you could configure apm-*-transaction* in siem:defaultIndex, and it would match on the apm-* Kibana Index Pattern -- something we're explicitly addressing in #52297.