Something along these lines was discussed but there is currently no good way to do it with custom layouts and I guess there wasn't enough interest to do anything about it.
Custom layouts use buildable names (e.g., "reactor" for a Reactor), which intermission points do not have. You could probably change that to entity type (e.g., "team_human_reactor" for a Reactor and "info_alien_intermission" for what you want), which could also make custom layouts much more flexible, but you'd need to substantially change the file format to make full use of the change (look at the spawn code).