Is there any reason that a FSB that is held on with set screws would be more accurate than on held on with taper pins? I ask because I have seen more than one manufacturer who sell complete SDM (Squad Designated Marksman) type uppers that use set screws instead of pins.

semperfi,
It's not that it's any more accurate.  The primary reason for a FSB with set screws is to allow you to set windage zero while having your rear sight at mechanical zero (in the middle of travel).  That way you haven't zero'd with the rear sight more to one side than another if your FSB is not exactly indexed.  This allows you equal opportunities to dial in windage when needed without having to compromise in one direction or the other.  

Also, allows "fine tuning" in that  you could set zero inbetween "clicks" of your rear sight (if you could hold that well).  Some rear sight assemblies for HP provide 1/4 minute clicks, so you're REALLY looking at a RCH level of tuning here.

This was originally developed for High Power Service Rifle competition, and found it's way, like many things, into practical application when needed.   SDM rifles are designed to bring to the field a level of accuracy not normally seen in a production battle rifle.

It's a crappy shortcut in my opinion.

www.jobrelatedstuff.com/forums/topic.html?b=3&f=118&t=264392

We're not talking about a "clamp on" FSB....   we're talking about a set-screw FSB.  The references in the thread you linked reference a clamp on.

Precision machining of the four points of contact into a barrel, and attaching a set-screw FSB is more handling and work than simply putting the parts in a jig and drilling.  It's not a shortcut, a clamp on, is.