The change is just for featured images, since that’s the only place in standard WordPress where an attachment ID is used.
I don’t plan to make any further changes at the moment but if you’d like to explain a little more and I’ll take a look again when I have some time.
To clarify: are you asking for multiple image attachment IDs to be saved to a custom field?
I’m assuming you mean a ‘normal’ custom field, since I think you discovered already that ACF prohibits any kind of background import into its special field types. Is that correct?
If so, can you give an example of your input data and how you’d expect to see it in the database wp_postmeta table?