Ok, let me summarize
the original app has data-sap-ui-appCacheBuster="./" in a bootstrap
the extension app:
has data-sap-ui-appCacheBuster="./" in a bootstrap
complains about view.controller
in sap-ui-cachebuster-info.json of extension app it has viewcustom.controller but not view.controller
BTW do you call
sap.ui.core.AppCacheBuster.register("/sap/bc/my/other/component"); for original application inside the extension?