See the comment here: #6289 (comment). PEP 695 type aliases can't be used for runtime typing, so we need to limit the cases in which we flag and rewrite them. For starters, we could consider limiting to .pyi files, where it should ~always be safe. We could then extend to "private" type aliases that aren't used in runtime contexts within a file.
Alternatively, we could just turn off this rule when keep-runtime-typing is set, and leave it as-is.