So this is a bug ? I checked the box that i want to use it for updating ?

It's not a bug, You need to remove attribute name with colon symbol. So "Legs: Custom,Color: White" Should be Custom,White

Since you want to update the internal reference so you can remove the product_template_variant_value_ids from excel or during upload click on x beside variant values

I understand ... but that sounds like a workaround to me.

It really feels like a bug.

If i export a file in a format for re-importing (By checking that box, so the id's get added). And without changing ANYTHING, i cannot re-import it without removing the prefix before the ':' , then that for me is not the intended behavior.

You can report that in https://github.com/odoo/odoo/issues