New York was and is very strict on their telecommuter rules, even before the pandemic. The New York Department of Taxation and Finance has provided guidance regarding telecommuting tax liability for nonresident employees working outside of New York because of the COVID-19 pandemic- employees telecommuting because of COVID-19 will still be required to pay New York taxes on income they earn.
Although a home office could meet the eligibility factors laid out in the bulletin, generally it would not qualify as a bona fide employer office outside of New York. An employee working from his or her home office would be considered to be working in New York for tax purposes.
You cannot provide any substantiation on or with the return and you are correct that changing the W2 is a cause for examination (note: your employer does not want to get involved which means they are unlikely to help support your claim if you are audited.) However, gather as much evidence as you can now and keep it with your tax records. New York is rather aggressive at pursuing this particular issue.
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