Canon Japan has replied and confirmed that this is a compatibility issue between MacOS 10.12.4 and later, Safari 10.1 and later and MacOS Canon Fax Drivers for the m249dw.
Since this is a compatibilit issue between Canon and Apple, I expect Canon to open a ticket with Apple's bug tracker RADAR and I will do the same.
For those following this thread, a workaround is available 3 messages up.
I will attach Canon Japan's email below
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キヤノンお客様相談センター <support@canon-mj.co.jp>
Dear Mr. LUK
We would like to express our thanks for your patronage of Canon products.
I am Toi of Canon Customer support center.
I have read your e-mail.
When printing on macOS Sierra 10.12.4 and later using Safari 10.1 and later, the Canon menu display (fax number input ‘General Settings’ tab display)
does not appear, instead a standard OS menu appears according to Mac OS app specifications.
For this reason, printer driver settings cannot solve the issue as you have confirmed that this is part of the specifications.
As a workaround, we recommend using another browser other than Safari or saving the file as a PDF and sending the fax from another app (Preview, etc.).
We hope this answers your question.
Best Regards,
Toi