fix(core): keep transient-context commands listed in shortcut settings

[SaKaNa-Y]

Description

Fixed an issue where the Close Panel shortcut entry would incorrectly disappear while opening and closing the Command Palette.

Linked Issues

Additional context

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commit: 5c36d80

[SaKaNa-Y]

Sorry, this issue was introduced after my fix for #502. After fixing #502, two side effects appeared: one is this issue, and the other is that users are not warned when binding the same shortcut to commands in different dock modes.