Are you trying to sell all of the shares? If so, the net gain/loss should be independent of what method you use (tho there could be a variation is long/short term distribution).
Have you selected a cost-basis method for your covered shares? Have you
previously sold covered shares?
I would check w/ VG to be sure but I would think since AVB is the default method for non-covered shares (and since VG is not reporting that info to IRS anyway), you could have different methods for covered and non-covered shares. You should check with them also about how you specify whether you are selling covered or non-covered shares. Sometimes the default is to sell non-covered shares first.