Jun Missions

Is there any reason why PS4 and I assume XBox Jun Missions only give 1 encounter compared to pc giving 3 encounters per Jun Mission/Jun Prophecy?

Here's what they said about it. You can find the whole thing in the synthesis league patch notes under "console specific"

"Areas which contain the Immortal Syndicate will only contain a single Immortal Syndicate encounter. As a result we are making the following changes:
Immortal Syndicate Safehouses now contain triple the rewards of previously.
You will get triple the experience of previously for deciding an Immortal Syndicate member's fate.
Interrogating a Safehouse leader now grants triple the previous amount of Intelligence towards accessing the Mastermind.
Tripled the number of Veiled Items you will get on average from an Immortal Syndicate encounter."