Try version 0.0.8+ of the repo modernizer plugin.
The prior version exhibited this symptom, and the way to work around it was to perform a non-global install of @adobe\aem-cs-source-migration-repository-modernizer in the same folder in which you're running the aio plugin from.
Ex.
$ cd project-to-modernize
$ npm i @adobe\aem-cs-source-migration-repository-modernizer
But that said, that was fixed in v0.0.8 so just upgrade to the latest version and you should be set.