Hi Ben,
I have a working theory now after thinking a little more on what you suggested. I noticed if a layer is fully qualified, meaning it goes all the way https://.../..../..../rest/parcels/MapServer/14 it gives a popup in Workforce, but if you use up to the MapServer part it doesn't give you a popup. Which is annoying because if you have a bundled map service it is generally bundled for a reason, but it not a total deal breaker to individually breakdown rest end points. I think it will be a little more work than I had anticipated, but workable.
Thanks for the suggestion, and confirming that indeed you can have a supporting layer have a pop up.