It's properly found but then it's validated only trough remote repositories. It's works with the XWiki Standard flavor because it's registered as known flavor which skip the validation step.
The possible workaround are:
- set the custom flavor as default UI, see https://www.xwiki.org/xwiki/bin/view/Documentation/UserGuide/Features/DistributionWizard#HUserInterface
- modify extension.xed to add the custom extension to the list of known valid flavors