It�s an interesting concept. Do you want to ease up data entry of the benefits of a multi select field, but you also want the benefits of a proper many to many relationship. It�s sort of brilliant actually
I believe that this can be done with a single automation. Make sure it would trigger whenever a parent record is created or modified and the multi-select field has been changed.
The first step of the automation would be to delete all the child records of the parent. That way you�re starting with a clean slate.
Now, presumably you know perfectly well what the Say, 10 choices are for the multi select field. So I would have 10 steps in the automation to create 10 child records. Each child record would of course be for one of the possible selections. Then using the existing relationship I would look up that multi select feel down to the child join table records.
I would then have a formula field on the child join table to calculate whether or not the child record created is indeed selected in that multiselect field.
Then I would have the last step of the automation bead to delete all the children of that parent record where the child records were created however they should not be allowed to remain in existence because in fact they were not part of the multi select field.