(Subject to disagreement, please be bold in editing)

The PRPG universe visibly diverges from the MLP:FiM canon, specifically, it includes all season 1 and 2 episodes except for "A Canterlot Wedding". (The game began in 2012 and obviously conflicts would inevitably arise as the show continued, in an uncontrolled way if a departure point had not been set.) Many elements (including most notably changelings) from subsequent episides have been individually canonized or referenced, however, and PRPG2 especially includes many references to G1 MLP content. As a general rule of thumb, 'world-building' items from MLP:FiM are likely canonical, but specific events are less likely to be.

PRPG1 and PRPG2 share a common universe until at least sometime after the end of PRPG1. At this point, there is the so-called good ending of PRPG1, which has the Golden Age changeling society coming to live with ponies openly, and becoming incredibly powerful. Conversely, in the backstory of PRPG2, this did not happen, and En-Netsusep invaded to extirpate changelings, causing the Catastrophe instead. So, PRPG2 and any PRPG2 one-offs after this point of divergence are not canonical to PRPG1, but the ones set in the past relative to PRPG1 are (e.g. the Eldritch Lore cycle excluding Special Agent Shiny Buttons, which is excluded because it didn't end like it did in the backstory.)

This would be the simple explanation, and, I think, the original intention when PRPG2 was planned, though there are other possible viewpoints. In PRPG1, an accomplished future-diviner saw the Isle of Yore in its post-catastrophic state, and the party also saw a vision of what was implied to be that future. This would suggest that it is in fact the PRPG1 Epilogue that represents the "alternative" universe, but there are other explanations as well, albeit somewhat contrived. (The divination might not have been true divination.)

Obviously, outside of the game itself where what the GM thinks is most salient, what is canonical is ultimately up to the individual reader.