I'm trying out a new map idea - basically everyone has a tech tree that only they have access to.

I've been able to do this by using a custom scenario distribution in the map editor. However, I want to be able to make each tech level successively more expensive than the last - so basically plop more neutral armies on the tech location. I can't find a way to do this from the map editor - only from the actual game creation.

This suggests to me that all I can really do is control starting positions, and would have to leave it up to the game creators to apply the proper settings? Or is there a way to encode in the map the appropriate 'default' settings?

The best you can do is to make a template with the scenario set-up, then include the URL to the template in your map's description.

Yup, i did that on my Succession Wars map. It is meant to be played with settings in the map description, but you can't force that.