On the other hand, if both players are buying Estates and naming Estate when they play Rebuild, then it's something of a crapshoot as to who ends up rebuilding Duchies and who ends up rebuilding Provinces.
Unless you have only two types of victory cards in your deck, Rebuild, like many cards in dominion, always carries with it a decent amount of randomness, regardless of what you name. I disagree that this strategy in particular makes it a crapshoot.
Assume you've won the Duchy split 5-3 and have at least one Estate*. When you want to maximize the probability of Rebuilding into Provinces, it's clearly best** to name Estate until you have at least as many Provinces as Estates. Once you have exactly as many and you are ahead, you still want to name Estate because Rebuilding Province->Province is better for you (since it brings the game closer to an end and removes VP from the kingdom) than Rebuilding Estate->Estate.
So only once you have strictly more Provinces than Estates can you even start to consider naming Province as a default. Whether you want to is a different question. If you have 3 or more Provinces, the only way for your opponent to catch up is to directly buy Provinces. In order to prevent this, you want to deplete the Province pile asap, and your best chance for doing this is again by naming Estate. So the only questionable spot that remains is having exactly 2 Provinces and one Estate, and I can't really provide a clear-cut answer to that case. I think it would depend alot on how far behind your opponent is and his chances (in terms of direct Province buys) of catching up. In any case, even this isn't a clear "name Province" spot to me.
So since in most cases it's best to name Estate, you might as well piledrive them to grab a few extra VPs and prevent your opponent from getting them. Sure, they clog your deck a bit, but that's not such a big deal as you're looking to draw one specific card, not hit a certain amount of money.
There's also more opportunity for the stronger player to track his shuffle and sometimes name Province instead of Estate.
I consider this a good thing, though I can see why you would think it's not
*When you have 5 Duchies and no Estates I think it's indeed best to always name Province and not buy Estates.
**Assuming for simplicity a fresh reshuffle with no green in hand.