Is there a way to install the DM with customized settings for reconciliation?

For example:

I want to have a filter in place and some field mappings changed around.

With the 3.6 I could 'record' this and add it but I'm not seeing this option with the new 4.2.x & MSI packaging format.

I have created an MST for the install itself but I'm drawing a blank on how I can get these customized settings in with the install.

Maybe they're stored in files that I can add/replace?