Apple’s response to my bug report:

Engineering has determined that this is not an issue for Apple to address.

Assuming this custom keyboard layout is bundled (.keylayout is inside a bundle like foo.bundle/Contents/Resources/foo.keylayout), then this could be as easy as inserting into the Info.plist's KLInfo_ dictionary:

<key>KLInfo_Qwerty</key>
<dict>
  <key>TISInputSourceID</key>

com.imgur.stack.keyboardlayout.Qwerty TISIntendedLanguage
en

If this layout is needed system-wide (i.e. including password input) it could be installed in /Library/Keyboard Layouts/, rather than the same location in ~/Library/

Please update your bug report to let us know whether this is still an issue for you.

If you have questions regarding the resolution of this issue, please update your bug report with them.

Please be sure to regularly check new Apple products for any updates that might affect this issue. Again, thank you for taking the time to submit bugs. We sincerely appreciate your input.

Apple’s response to my bug report, in which I was asking to make it possible to remove the system default keyboard layout if another one is selected through System Preferences:

Engineering has determined that this is not an issue for Apple to address.

Assuming this custom keyboard layout is bundled (.keylayout is inside a bundle like foo.bundle/Contents/Resources/foo.keylayout), then this could be as easy as inserting into the Info.plist's KLInfo_ dictionary:

<key>KLInfo_Qwerty</key>
<dict>
  <key>TISInputSourceID</key>
  <string>com.imgur.stack.keyboardlayout.Qwerty</string>
  <key>TISIntendedLanguage</key>  
  <string>en</string> 
</dict>

If this layout is needed system-wide (i.e. including password input) it could be installed in /Library/Keyboard Layouts/, rather than the same location in ~/Library/.

Please update your bug report to let us know whether this is still an issue for you.

If you have questions regarding the resolution of this issue, please update your bug report with them.

Please be sure to regularly check new Apple products for any updates that might affect this issue. Again, thank you for taking the time to submit bugs. We sincerely appreciate your input.