It doesn't matter whether the Source and Destination is different OS Flavour, at the end of the day these are two independent copy with different Deduplication association.
Note - even if you use a mix of Windows or Linux on a single copy it will still work, it all depends on how the Storage is presented. (i.e. if the disk library is Network Share, with CIFS & NFS multi-protocol, both the MA will still be able to read/write the data, the CHUNKs do not change between different OS)
For best practice, in most case you would segrate using different OS to minimize complexity, but it will still work if you do configure them under one GDDB)