Even though there is a .config file alongside the .exe, there are no useful settings within.

BUT....

A little secret. Press and hold the CTRL Key and then wheel up/down on mouse when editing the prontoscript.

TADA! It's magic.

The change persists until such time as you move to another object of different type. So, if editing a page script and move to Advanced tab on another page, increased size remains. If you then move to a button and stawrt editing that in the ProntoScript windows of the 'Actions' tab, the size will persist across different buttons.

I found this by accident when first dealing with PEP2. I wish the changes persisted across edits but as is a CTRL + Wheel, is really easy to zoom up/down.