Thanks a lot @JotikaT2 ! In this case, even though seemingly NY is pocketing more than just NY-sourced income, I shouldn't care since I wouldn't be double-taxed.
However, this does put me in a position where I'd have to pay NY state significantly more taxes than my NY withholdings. This would have me pay NY underpayment penalty. Is there a way to pay NY state just for NY-sourced income?
Things are made even more complicated by the fact some of my compensation is in RSUs. According to my employer, taxation on RSUs is proportional to where they "spent their time" vesting. The RSUs have been granted a while ago, so they spent most of their vesting time in California. This way, for RSUs that vest after my transfer to the NY office, my employer withholds California taxes off ~95% and NY taxes off ~5% (this split will shift towards less CA and more NY over time...). This further increases what appears to be "under-withholding" NY taxes, unless there's a way to make NY recognize this allocation as the correct one.
