$wgEnotifMinorEdits causes email notifications to never be sent for minor edits. There is no per-user override, which means it will no longer show "Email me also for minor edits of pages and files" in preferences.
$wgEnotifMinorEdits is false throughout almost all WMF wikis.
I think it would be more intuitive to set it true everywhere.
The wikis with $wgEnotifMinorEdits already true should start with $wgDefaultUserOptions['enotifminoredits'] also false (since it is now), but perhaps be asked if they want it true (that would change the current behavior for them)). Other wikis could also change $wgDefaultUserOptions['enotifminoredits'] later if they wanted.
That way, it would be default-unchecked on most wikis, and people wouldn't get emails, but they could still choose to. It is one more preference, but it's tucked in a section with 3 checkboxes already, and I think it's a net benefit to let people choose.
This also works around T29884: enotif doesn't send email if page on watchlist edited following a minor edit and enotif not configured to send minor edits. somewhat (since you can at least opt in). With T29884 still broken and without this, the situation is quite bad.