ALT 258 Smithfield is definitely a sign-o. That one, without a doubt, should be switched to the state system.
ALT 220 becomes a case of do you go with what it's signed as, or what it really is? One could argue that we have precedent for the latter...specifically the hidden Interstate routes.
I have no problem with this outcome - I have never seen a VA 220 ALT posting going back 25 years.
As for rectangle postings, this is not a statewide thing but a district thing. Some districts use the white rectangles heavily on all primary routes and some basically only on secondary internal intersections.
At least two white rectangle-only 3xx routes are waypoints on the state route system in TM (VA 375 off VA 3; VA 388 off VA 20).
As for VA 228 Truck, the CTB has stopped recording most of its changes to the primary system. VA 228 is no longer posted within Herndon so it may be routed on Herndon Pkwy already, though the 2014 traffic log shows it still through town. I can put together a VA 228 Truck file this evening as well as fix the 258 ALT stuff.
VA 319 is not shown as a waypoint at either of its US 1 junctions (nor is it on the VA 142 file), but VA 357 is. There are some things I will do with the 3xx routes (331 is posted in a shield but not in TM either) with my inclination to omit routes that are unposted entirely.
Virginia had up until pretty recently been good about going to AASHTO for the Business routes though I don't recall seeing US 460 Bus Grundy go through there. Virginia hasn't commissioned a US ALT route since the 1950s.
If you wanted to get REALLY nitpicky, the F-series routes are technically primary routes in Virginia. But I have no intention of including them even though some are signed with circle shields.
Mike