A minor detail that seems to have been missed:
When the taskbar (enhanced in my case) is on top, in order to better match how the taskbar used to behave on older Windows versions that natively supported the position the System Tray icon needs to be inverted from how it is currently:

To be clear:
- Currently:
- Tray closed - Arrow points up
- Tray open - Arrow points down
- Correct:
- Tray closed - Arrow points down
- Tray open - Arrow points up
When using Start11's left/right align feature, the System Tray icon is properly turned sideways and points in the correct direction (right/left respectively), so this icon is definitely something that's already setup to be modified by Start11 and as such I imagine that a tweak just needs to be added for the top configuration.