I have the same experience (that System|Preferences|Keyboard -> Layouts ->Other Options... configurations do not apply to hotplugged keyboards).
I am not 100% sure that this is the same as .xmodmap files not applying, but it has been one of the virtues of Ubuntu for me that I can configure my desktop experience with the pointy-clicky rather than learning YADF (yet another dot file).
I agree, from reading the descriptions, that this bug might be related to Bug #289781.
I have the same experience (that System| Preferences| Keyboard -> Layouts ->Other Options... configurations do not apply to hotplugged keyboards).
I am not 100% sure that this is the same as .xmodmap files not applying, but it has been one of the virtues of Ubuntu for me that I can configure my desktop experience with the pointy-clicky rather than learning YADF (yet another dot file).
I agree, from reading the descriptions, that this bug might be related to Bug #289781.