I don't recall the exact numbers because it's months ago that I did the simulations, but Rebuild beats Cultist-BM and in general Shelters have a slight but practically negligible impact on Rebuild's viability: the effect is so small that you're unlikely to ever encounter a kingdom in which it matters, and if you do, you won't be able to notice it (unless perhaps the opposing strategy is known to be close in the first place and itself benefits significantly from the presence of Shelters).
Contrary to common belief, Rebuild is still very strong (but indeed a bit weaker) in Colony games: you can end the game on Provinces just the same, so a competing engine doesn't just need to be powerful, it also needs to be fast. The only thing about Colonies is that the Rebuild player won't be able to get half of the VP as easily, so that an engine that can grab enough Colonies before the Rebuild player can end it is now competitive, but, say, a Goon's engine that's slightly too slow in a Province game will be too slow to the exact same extent if Colonies are on board.
And Rebuild-Jack > Rebuild > Jack is certainly a win for Rebuild; that Rebuild-Jack beats Rebuild has nothing to do with the power of Jack over Rebuild, but rather with the power of Jack over Silver.
As for Rebuild vs. Witch: yes, Witch-BM beats pure Rebuild (though not by 60-40), but in practice you'll be playing pure Rebuild only rarely, as there's usually a card that supplants it, and adding either a Jack, Horse Traders, Monument, Tournament, Rogue or Graverobber to a Rebuild strategy beats Witch for sure, and probably also Swindler, Scavenger, Scheme, Warehouse, Baron, Navigator and maybe even Chancellor and Oasis. Because these cards don't help the Witch player to the same extent, Witch can still be safely ignored on many/most Rebuild boards (unless Witch into Rebuild beats those strategies, which is something I haven't checked but is certainly possible).