IMHO, if you need a configurable product with over 2k variations, then something might be fishy in the way you are modeling the business requirement. Sure, there are business over there where this solution might sound like what they need, but think of the resources that are being consumed when working with such a large volume of variations:
- when a child product updates price or inventory data, the parent is also updated;
- your admin crashes when you are performing a save, my assumption that it will continue to do so as the request either takes too long and is killed by the server or it eats up the memory;
- also, on frontend, a page load without cache will be in trouble;
- UX-wise, the interaction of the end user with this product sounds like a big no-no.
You could try to update/ save the product via API, but it's a very tedious job to keep all the children product data JSONs in a valid shape and format.
My recommendation would be to try to break down the parent product somehow.