The problem was that this webpart view was not within the context of my custom page type. There is a dependency of page type query in (page type) > Queries which needed to get modified. So if you're having this problem in the future you might want to check your page type queries and make sure you're pulling the new page type field.
More experienced Kentico people can chime in here, but I think this needs to be done when you're using a page type transformation outside of a page of that type, or if the transformation has a page type query dependency.
I know this may not be of much use, but it was what the issue was for me, so posting it just in-case you want something to check.
EDIT: Just a bit of extra information
I was using Universal viewer with custom query webpart and the query that I needed to modify was in the content textbox.
Part of my mistake was assuming that because the "generate default transformation" contained my page type field bool, it would thus be available in the transformation; this was not correct. The data comes from the content query (obvious in hindsight).