You are getting a little sophisticated here.
The original mouse cutup was to keep only the ir circuit and discard the rest.
Thus the signal was (and is) raw grey code. If the pc board is also included, then, yes,
the communications protocol must be followed. I guess it is a simpler solution as
the mouse can be used intact...however, the optical or laser mouse is a bit different.
It is not so easy to recover the plain grey code generator. So using the protocol on them is
probably a necessity.
I presume the important thing is to distinguish which type of mouse one is working on. Once
upon a time there was only one...now there are many. They vary.