You have to drill holes thru the barrel for pins, and there isn't much room for that. Barrels can and have been distorted from it with the rifling pushed out of shape. It's a gunsmith level operation at best. The milspec on the design was to prevent soldiers from monkeying around with the parts, or having screws back out over a 20 year service life. It's considered a "fleet" maintenance issue with 7 million rifles in the system.
YOUR rifle, not so much. Set screws allow disassembly in the future and fewer issues.
There is also the new ITAR interpretation that may require smiths to pay a $2000 yearly fee to alter any part. Set screws are a simple adjustment, pinning is a drill operation and materially changes the as-shipped nature of the barrel.
I expect that barrels won't get pinned FSB's casually removed or installed in the future because of this. The traditional gun owner, however, is likely to discover a major source of heartburn over it as most proprietary designs aren't lego and I suspect things are going to get ugly. Filing, buffing, stoning, fitting locking lugs, etc can and likely will all fall under it.
It's the STATE department who changed this. Not the ATF. Think who used to have that job as Secretary of State.