Another great episode!
As long as the end of the shaft doesn't interfere in any way with the rod, I see no reason to cut it back.
Just a question .... why did you do the taper reaming by hand instead of using power at low RPMs? Perhaps just so you didn't have to bother with the critical alignment of setting it up, which can often take much longer than the actual work itself, especially when it is a quick and easy job like this one?