I would argue that the idea that these roads are being bypassed due to their at-grade intersections would further deter warranting making them trunk, since it can take up to 20 minutes more to follow a congested stop-and-go thoroughfare than just staying on the Interstate.

But regarding your justification that this meets trunk criteria, due to its intersections with other roads that I 66 doesn't link; pretty much every other US highway paralleling an Interstate does. US 1, 11, 13, 58 60, and 250 all do this in Virginia for significant sections of their routes through the state. There hundreds of other examples outside of Virginia too just like these. In many cases, these highways also have grade-separated junctions with other roads, such as US 1/VA 3 in Fredericksburg, US 60/VA 105 in Newport News, and US 13/US 58 in Norfolk. US 29 has a freeway-like junction at Fairfax County Parkway and West Ox Road, but you still have to cross signalized intersections to get onto an actual freeway like FCP or 66.

If the secondary routes these highways that connected to US 29 and 50 were other trunk routes, then that would most definitely make these roads trunk, but since the only other road that is just as important as these roads is Gallows Road (which is primary), this can't really be used as a justification for making them trunk.