You can bleed a master cylinder in place. The reason I suggested
bench bleeding is so that you are using clear tubing and can see
if air is being introduced with some problems with the deep part of the bore
and the seals. Two of my rebuilt jobs would drag in air past the seals on
one or more ports. This shows up right away at the bench vise, and how can you see it when it's hooked up to your brake lines.
It's not so hard to yank the M/C and reinstall, you do get some mess of course
and have to use more DOT4 ,maybe a pint.

The company seems to have done better with this last M/C,
maybe after they kept having to replace for free.

I'm guessing that a four port M/C is maybe more trouble than normal to rebuild.
Plus if they dont install a new sleeve for the bore then it's probably not
really a rebuild job at all, maybe they just replace the seals leaving you
with a problem bore?