The chat window continues to work so if there was ever a system limitation (because loading screen) I don't think it would still apply.
I can see some logic in making sure the player's eyes are front & centre as they arrive at the new system, but other instance transitions just pull you back to the main view so I don't think it would be this either.
Navigation & targeting info not being available (most of the left panel) is understandable, but most of the right panel tabs could be shown, even if it's just to view & not change your power priorities & firegroups.
However it's only a few seconds so not a big deal for me.