"My concern is that deviating from the employer's W2 state wage might be non-standard and a red flag (is it?) but at least if I go with my amount calculated from my approach I can fully explain how I arrived at my allocation. Should employer W2 state wages be treated as fact when filing returns?"
A piece of data in the hand is worth two pieces of data in the cloud.
If the employer's allocation is at all plausible, I would go with that and not worry about it. It is unlikely that either state taxing authority will give it a second thought.
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