> But if 2-9-3 really had been isolated from its relative for a quarter billion years, enough random mutations in the rDNA should have accumulated for there to be a difference of at least 50 base pairs

Occams razor definitely points to this just being a sterilization problem. But it would be funny if the bacteria was just way more stable than people expect.

Ribosomal DNA is extremely highly conserved and normal random mutation models do not predict it's changes well at all.