You are asking the correct questions, and I appreciate that you seem to have thoughtful application.
The problem with the Convenience of the Employer rules is that it purposefully and complet...
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You are asking the correct questions, and I appreciate that you seem to have thoughtful application.
The problem with the Convenience of the Employer rules is that it purposefully and completely ignores the realities of remote work. Your employer "assigns" you to a work location because that is the main criteria New York uses- the "headquarters" or office location of the employer. For larger companies, they are able to assign their remote workers to a non-New York location to avoid the convenience rules; but if your company does not have offices in other cities this is more difficult.
You have identified the biggest flaw- Illinois does not give the credit for taxes paid to another state if the work is physically done in Illinois, so you could be taxed twice on that income at the state level. There are court cases but as I said before New York is actually winning these. See Zelinsky II—The Continuing Saga of Remote Work.
It used to be that they did not scrutinize as much especially with lower income, but in general that is not the case anymore- and New York does not only go after the employees, they can ensure compliance by the employers exactly in the way your employer has it set up to do withholdings for New York state only.
You can choose to allocate the wages and hope for the best (no New York audit), and I apologize for being a bit meekish because it is obvious you have good knowledge and are not in any way trying to get away with anything but rather looking to do the right thing.
@jackkgan