The information you quoted with regard to the IRS presuming that the income is wages for the first three years is a qualification for claiming the Qualified Business Income (QBI) deduction. This is not related to whether you qualify to claim expenses for a home office.
If you are working as an independent contractor (whether for a former employer or not), you can claim home office expenses without a time restriction as long as the qualifications for the home office deduction have been met.
You may want to consider amending your prior tax returns if you have not been claiming this deduction already. You can amend 2019, 2018, and 2017 at the current time.
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