This is one of the ways in which i believe portrayal > feats to judge intended strength of characters.
You can very well make the argument you've made and follow through with base Yamato ~ Ace, thus reason that Yamato with her DF would be that much stronger based on what you've seen on panel, but at the same time you agree that Yamato overall being Ace's equal is what Oda's going for.
Yeah, but I think the most sensible interpretation was that Yamato did not have or wasn't using her Devil Fruit back then as opposed to Ace being equal to a hypothetical Hybrid Yamato.
I don't think we can assume that.
If for example, Yamato couldn't transform because of the shackles, then Ace ~ Base Yamato is the same as Ace ~ Yamato. The same would hold true if Yamato
could transform, but was just unwilling to do so.
If Yamato only ever fought in Base, then being equal to Base Yamato is being equal to Yamato.
I think something like that fits best with the portrayal of intended equality and the implications that Yamato never transformed vs Ace. Trying to assume that Ace = hypothetical Hybrid Yamato is stretching things a bit far IMO. Like Oda could have hinted at her using her Devil Fruit (perhaps silhouetted) if he wanted us to think that she did.