Hi,
I think, I'm not sure that there is an issue with an option within the Custom Fild meta box option (page name : Edit Field Group -> Tab : Settings).
When I set Position : Side, the metabox stay under the content box.
Settings (I set "Side" in my setting page and not "After content") :
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Result in Post Type edit page :
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Thanks for your help 🙂
Regards
Axel and Adrien