The issue is present in betalabs 1.28.0-alpha (2fc4a0b) on the Notifications flyout and Special:Notifications.
The screenshots are from iOS 9.3 iPhone 6

This is better now that have only 1 secondary link outside of the menu.

Why is the dotdotdot menu displaying as a standard mobile menu (at the bottom) in the flyout but as a desktop menu on the special page? It's causing a horizontal scroll bar in some cases.

This was just fixed with these two commits:

• Mobile version of Special:Notifications https://gerrit.wikimedia.org/r/#/c/302369/
• MobileFrontend (the mobile popup) https://gerrit.wikimedia.org/r/#/c/302370/

It does exactly what @SBisson suggested -- it brings the number of prioritized actions (the actions outside the dotdotdot menu) to 1 instead of 2 in the mobile experience.

This isn't a perfect solution, but it should definitely help for the vast majority of cases.

In T131498#2516580, @SBisson wrote:

Why is the dotdotdot menu displaying as a standard mobile menu (at the bottom) in the flyout but as a desktop menu on the special page? It's causing a horizontal scroll bar in some cases.

Yes, I just saw this yesterday with @Etonkovidova -- there should be a separate bug about this; we need to add the global overlay and place the dotdotdot popups in it, like we do for the mobile popup.

@SBisson and @Mooeypoo comments are in a separate task now - T142013: [mobile] the dotdotdot menu layout improvements on Special:Notifications page.

Checked along with verifying the fix for T141788: Formatting problems with Special:Notifications on mobile. Also checked hewiki in betalabs - no specific issues for RTL for this case.