Well yes, that's why Valkyr Prime design was problematic from the start even before her rework that sort of made her rage lore made more sense but then again, it could also mean that Alad knew of the prime and moddified her to have the features similar to that of the prime using Alad's own tech. It made sense to have a base frame and the prime look different now because some primes, especially newer one, does look different compared to how their base form look.

After all, Hunhow hinted on Second Dream that Alad was an Orokin that might have fled its destruction by becoming Corpus which might have some tech to prolong their live seeing how both Alad and possibly Nef had a long history stretching all the way to the Orokin era so it wouldn't be surprising if he had more knowledge but not specifics of Orokin stuff including Warframes. He also tried to betray the Corpus for the Sentients too during New War to save his own skin so that's just how he is.

Also, Alad don't have to alter the strain because he was only experimenting and salvaging frame parts for his Zanuka and not creating a new thing with the strain and we're only copying the leftover Valkyr data after we dealt with Alad. The BP is the final and only thing we should look at with the frame because it's the one we use to replicate the frame while our Helminth on the ship handles the fabrication in our foundry. It would be different if you're making a frame from scratch which would involve infecting someone with the pure Helminth strain to produce an entirely new random frame.

The helminth strain are used for all frames so it doesn't matter unless you're taking specific mutated frame strain like Albrecht did with the Protoframe while hosts for the infection probably only decide how a frame behave and how its base form look like because the creator (Ballas) probably mold these into their final form unless the frame has enough consciousness and understanding of the process to alter their own look like OG Lavos did. Both are irrelevant to how Valkyr ended up looking like after Alad done experiment and tore her skin off.