Many lists play now Jester Cap alongside Unmoored Ego. In many cases even if you have a couple of Artifact hate (i.e. shatterstorm) you’ll never be able to cast them. Another option that is adopted is Darksteel Forge. They are actually less fragile than they seem. A good player can achieve MW% greater than 60% against all tier decks (see sussurrus_mtg twitch streams for reference).
That said I agree that it will remain a tier 2 or less deck that can’t be the police deck someone prays for.

I doubt it. As I note, it’s a very fragile prison deck. More robust decks like Lantern and previous versions of Whir have had their moments, but they’ve all fallen away over time since they all lose to Shatterstorm. Once the Phoenix players start adjusting to this counterattack, Whir should fade again. Also, given how Wizards doesn’t like prison very much, I doubt one doing well would be seen as a positive to the status quo.

Do you think the rise of the whirr prison deck will be enough for wizards to see the players adjusting and not take action against cards in the pheonix deck?

I don’t think anything’s actually changed to be honest. Every Modern PPTQ season that deck resurfaced in some form in Colorado, usually WR Sun and Moon. It was great as a surprise deck and occasionally did well but only for one tournament. The problem isn’t the metagame, the deck is just anemic. It may not get hit by hate like artifact prison, but it’s just ends up being worse each season. Much like the Whir Prison deck it just folds to Cryptic Command but it’s worse because it doesn’t have the benefit of all the artifact cantrips to make it consistent. Even with Idyllic Tutor it isn’t able to lock out opponents as consistently and thus just fails more often.