That's what I have heard from a LOT of people in the boating business and I certainly strive for it when aligning...
However in recent years...guys I really respect in this industry have smiled and smirked when I bring it up....
More than one has said that the average engine rubber isolation mounts allow way more motion of the engine than that .001" per inch of flange...I tend to agree after seeing many engine installs and shaft suppots from cutless bearings to struts, etc that certainly induce way more than that .001.
So I don't sweat it when aligning...I do a quick one looking for tolerance...then move on...
Heck it's usually a struggle just to hold the sag of the shaft , redo after the rough says it's OK, then engage the lip of the tranny flange into the hollow of the shaft flange, redo the measurement and hope I'm on target...