1. Did John see God the Father and the stone tablets? In which case he saw the OT ark.
or
2. Did John see God the Father, and His Son Jesus Christ? In which case the OT ark is a non-issue. And keep in mind that Mary's care was entrusted to John and arguably he would have been very close to her.
Well, that's all well and good, but I cannot quite see the significance of John's vision to archaeological questions about the Temple Mount.