You can have multiple load points.
You can only have one save point, although it is possible to manipulate the save point during the saving of specific field groups using a combination of filters ‘acf/update_field_group’ and ‘acf/settings/save_json’
ACF loads JSON versions of field groups first. It then loads field groups from the DB for any field groups that do not have a JSON file based on group key.
The only reason that fields registered in PHP would not override JSON is if the group key of your group added in PHP matches an already existing group key. Group keys and field keys in php loaded groups must be unique and not match group keys or field keys that exist in other field groups.
