How can I set up a public transport route_master in Potlatch 2 ?

You'll need to do it from Potlatch 2's "advanced" mode, since Richard explains in a comment here why it's unlikely to be added as a preset.

• In Potlatch 2, click on the desired item.

• Click "Advanced" at the bottom left.

• To add to a new relation click "Add To / New Relation / Advanced" and then manually add the tags that you want using "add".

• Save as normal, and your new relation will be created along with any other data that you've changed.