Unfortunately, if Vanguard isn't managing the SEPP for your SEP, then they have to report this as code 1 and there isn't really anything that can be done that you're not already doing.
I would keep the documentation of your substantially equal periodic payments handy and be prepared to send to the IRS each year until you've gotten to the end of this sequence. I agree that the IRS is not likely to reach out again once you've satisified their initial inquiry, but for each year that your code doesn't match the one on the 1099, you'll likely get a notice.
This is because it's an automated system that generates the notice based on the mismatch.
Then, it takes a human to see the issue and resolve it. If it weren't automated, the person processing it could likely view your prior year file but IRS systems don't generally "talk" to each other across tax years, so the system won't likely ever see your history, and will continue to ask about this on an annual basis.
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