Hello,
Whether the custom fields are stored in postmeta or custom table, isn't that a Metabox matter?
Yes, the custom field value stored in a custom table is a Meta Box matter, but does it work with the standard WordPress editor?
If it doesn't work with Make, I'm not sure how Make works with WordPress. Maybe it inserts/updates the post data and custom field via Rest API and it isn't compatible with MB Custom Table functions.
If it is possible, please setup a clean environment and share the information via this contact form https://metabox.io/contact/
I will inform the development team to check it and see if we can improve something from our side.
Thanks.