Because of issue MC-3643, when I Command-Tab back to Minecraft, if I press a number key, instead of selecting that entry in the hotbar, it saves my current hotbar to that number key.

Before this saving hotbar feature, the fact that modifiers would get stuck on was a minor annoyance. It would only really have any major effect when in chat and would never cause any irreversible action.

But now that Command+Number has meaning, this has become a serious usability problem, because it now can cause serious disruption to workflow by wrecking carefully-organized saved toolbars.

I suggest either (a) actually fixing MC-3643, or (b) choosing another modifier key for the "save" feature. Instead of Command, for instance, you could make it the Alt/Option key. This would once again mask this stuck modifier bug and stop wrecking saved hotbars.