As a practical matter, since there are no official storylines that relate the Tri-System to the Confederation, any references in some fan-created story or mod would of course be speculation.
But to say simply that P2 occurs in the future and can therefore be ignored is problematical, because the basis for dating the game around 100 years after Prophecy is the Tri-System’s own calendar of dates and years and the assumption that those are the same as the Confederation’s calendar. But how can that plausibly be? Only, I would think, if the Tri-System was previously a member of the Confederation (or at least had some pretty significant and involved contact). That possibility is certainly hinted at by EA when it describes the Tri-System at the time of P2 as not “currently” a member of the Confederation. But if the two were indeed so “entwined” earlier, then the possibility exists that relationship began near or at the time of Prophecy, if not before.
On the other hand, if the assumption about the calendars is wrong, then the events of P2 cannot so confidently be dated, though I would think they are then more likely than not to be closer to the time of Prophecy, if not concurrent or even earlier. (And in this case, we’re not presuming any significant prior or on-going contact between the Tri-System and the Confederation.) Certainly the “mystery ship” in the game that appears to be a Talon is suggestive in this way.