I do think the built in margin over stall for the published Vx is most likely. Perhaps in Aviat's opinion, Vy doesn't get close enough to stall speed until you're high enough to be well clear of terrain in most cases to bother applying the same correction.
Here is a an aerodynamics project we worked on during University for the Van's RV-7. Sea Level, flaps up, 1800 lb (MGTOW), ISA standard conditions:
Published Vx = 66 KTAS.
Calculated Vx = 58 KTAS
Vs = 53 KTAS.
Compare that to Vy, which we calculated at 84 KTAS and was published as 84 KTAS. The inflation to published Vx was undoubtedly Van's making a decision to prioritize stall margin over climb performance. If an experimental manufacturer/builder does this, it's almost certain a certified manufacturer would, given the liability differences.
