Thanks a lot – this is really interesting!
I think the answer I just posted on this thread already goes in a similar direction – essentially, all you need to do is export your images and add your questions to them programmatically.
Keep in mind that Prodigy’s annotation interfaces are intended to let the annotator move through examples very quickly and focus on one decision at a time. So you can use this to your advantage by framing each decision as an individual task that can be answered by one or two clicks or key presses. You might even be able to reframe some of the questions to make them even quicker to annotate – for example, by phrasing them as binary decisions. Ultimately, a lot of this will come down to experimentation – and being a little creative 
The use case you describe – i.e. having domain experts like radiologists doing the annotation work – is definitely something we’ve had in mind when building the tool. The main focus here is getting most out of the annotators time, helping them focus on what really matters and let the computer handle the repetitive and tedious aspects of the annotation work wherever possible.