It's the version of Shirou that Muramasa possessed as a Pseudo-Servant, yes, but the implication of those CEs are versions of the characters at the peak of their personal power. So it's a case Shirou "at his peak" also makes a good host for Muramasa.
Muramasa uses a similar but slightly modified version of the LZO design.
I assume Prisma Cosmos doesn't count?
More sad that the old big3 ce got power creeped so bad. Unlike Picos, black grail, and kscope which are still very old cards are still relevant today even in JP.