This is a strange issue. But essentially, we import a repo with notifications disabled but with some repo's users still get emails for historical activity.
Our noted reproduce steps by the gent doing the imports:
Repository we have noted this behavior with: https://phabricator.wikimedia.org/diffusion/UINF/
Example user who has history in that repo who complained of email flood: https://phabricator.wikimedia.org/p/lcawte/
Example of their history: https://phabricator.wikimedia.org/diffusion/UINF/browse/master/lcawte
A user who has chosen to not receive emails for new commits via audit seems not to get these emails.
https://phabricator.wikimedia.org/settings/panel/emailpreferences/ -> Audit -> "A commit is created" -> Ignore
This does keep them from being sent for that particular user.
Note we are still running Phab at commit 8bb390fecd0a849e9e45eb309ee9822d3f55fc60