Practitioners have been processing negative payroll contributions in order to correct over-deposited amounts during previous payroll cycles for the longest time now. I remember back in the early 2000s (or late 1990s) arguing why it was best to correct under the separate transaction and adjust for earnings as opposed to merely disguising the error through a negative payroll contribution. I, distinctly, remember being over-ruled on that argument (at my employer) for sake of operational efficiency. I find it interesting that the conversation, now, is about everything 'we cannot do'. Anytime I encounter a situation where every alternative is fraught with issues, then I suggest that a VCP submission will give you all the comfort you seek. The argument, then, is not about what can or cannot be done (because a Compliance Statement will settle this), but more about whether the level of comfort is worth the cost of the submission; especially when it involves a correction method already being discredited under a self-correction routine.
Good Luck!