Yamato is as strong as the plot demands her to be, even if a yc 1 at the start of wano got neg diffed, this does not mean that any yc will be neg diffed also, if the plot favors them, they will fight kaido 1v1 for as long as it will be needed.
Let put Katakuri in Luffys place, he gets neg diffed at the start of wano, and then he will fight equal with kaido when the things matter, its clear that luffy wasnt supposed to defeat kaido in his first encounter.
Yamato will do good, way better than yc level luffy at the start because now the plot matters, and her father wont go for the kill, Kaido still has great plans for Yamato even now, and probably even in his last moments when he gets defeated.
So yeah, Yamato is at that yc commander level, and if the plot demands she will stall kaido for some time.
Another exemple is with Kid, he showed nothing that puts him on the level of a yc1 commander, yet he suddently started to stall big mom on his own for some time, till trafalgar arrived, the same happens with yamato right now. Kid has basic coa coo and coc+his metal devil fruit, and apparently this is enough to stall a yonko, so chill dudes its not big deal if Yamato stalls Kaido for some time.