@Denis yes, it is totally safe. The code fully expects to encounter unaligned files and will work with them normally, without using block cloning functionality. There are many valid scenarios when unaligned files may appear in ReFS 3.1 repository, so this has been thoroughly tested and is fully supported.
QC made sure it is blocked in PowerShell because it is blocked in UI, with the latter implemented based on my request
I just did not want users to be able to easily mess up block cloning without realizing they do, making the following few synthetic fulls overfill their backup repository as the result.