Hey Keith, thanks for the insight. I ended up with a similar aproach, using repeater fields.
First I css-numbered the gallery images. Then I created a repeater in the post (not in the image) for the captions. Each repeater field will be the corresponding image caption.
It’s still not the best solution, as the user will have to change a different set of fields for gallery images, but considering how WordPress works, this at least get the job done.
This certainly is something I’m willing for. Maybe a checkbox that pops up when changing field name, asking whether data should be kept or not.
The CPT UI plugin has a similar behaviour.
