I noticed in our codebase after updating to 1.10.1 and removing the deprecated registerLoader('class_exists') call that our custom annotations were not recognized anymore. Getting a "The annotation [...] was never imported. Did you maybe forget to add a "use" statement for this annotation?" error message, though there is in fact a use statement.
I thought pull request #271 would fix that, but it appears that class_exists is not called.
I think I narrowed down the cause to the registerFileUsed flag. In the AnnotationReader constructor is a call to registerFile, which means registerFileUsed is always true, which results in the class_exists fallback never being called.