Had a player receive a Miraidon and our server still has it's default stat file with the undexable tag. Other custom pokemon species files that have been given undexable are also still obtainable via the '/pokegive random' command after testing.
I'm under the impression that undexable pokemon were not supposed to be given with '/pokegive random' but only when specified by species.
The Miraidon was obtained by this exact command: '/pokegive Player random legendary'

Thanks for the report. I was able to reproduce this using the same command you used. Moving to internal