For me, a lot of it comes down to the specific way he dodges The Question as it's presented in 'Cross' ; I think Father Flynn wants Jason to come to his own conclusion, whatever conclusion that may be - and there's something in that, especially when played against the way that Jason's character is so burdened by the expectations of other people. For me 'Cross' is never framed - at least not in it's entirety - as an ultimatum until Jason himself makes it one.

It's always coming back to the "never spoken, always heard" of it all - I think the way Claire treats Peter in 'See Me' works really well as a parallel to the way Father Flynn treats Jason in 'Cross' ; but where Claire is afforded more nuance in the form of 'Warning' there's much less time spent with Father Flynn, and in fact 'Absolution' is the next time he's really present after 'Cross'.

Which is not to dismiss Claire as a character or her growth*, or to imply equivalence ; I'm just proposing that Claire's motivations for dodging Peter's attempts to come out to her mirror Father Flynn's motivations to dodge Jason's attempts to come out in the context of their conversation - "Mom, I'm-" "Peter, please [...]", as opposed to - "Do you know what I'm-" "Yes.".

Both adults know what is being said, and both adults know why it is being said as well. And while they may have different motivations as to ignoring the reality, and hence not entertaining the consequences of the situation, the implicit statement is still the same ; I don't want to face the consequences of you being Queer.

For Claire, that consequence is feeling as though she has to chose between her son and her religious beliefs.

The thing is, Father Flynn has already chosen his religion. I do believe he knows this, and similarly I believe he knows that some of the kids haven't - Peter & Matt in 'Confession', for example.

And I think connecting 'Cross' back to 'Confession' is a key point as it relates to the way Father Flynn interacts with the main cast as a whole - the way it's presented in 'Confession' is dismissive, played against the intensity of 'Cross' where confession is seen as a much more crucial moment. However, the message being relayed is ultimately the same.

"Questions of doctrine are best left to greater minds than yours" vs "You know in your heart that the teaching is clear" seem like statements at odds with one another, but at their core both are saying that the rules are in place for a reason - it's not Peter's or Matt's or Jason's job to think about why, and it's in their best interests to get used to that fact.

Father Flynn - and yes it's by virtue of his character's function as a stand in for The Church as an entity that he's painted as this perfect pious face - never reads to me as mean-spirited. Truly, it's not until the second half of 'Cross' where he's all but forced to give Jason the ultimatum he's seeking (because truthfully that's what it is - it varies from production to production, but by and large 'Cross' comes across as a final crossroads. By the end of the song Jason's decision is made - even given the context of 'Two Households', and the way his pleas to Peter to run away are framed, it is 'Cross' that is the point at which his fate is sealed).

We'll always ask ourselves, if there was something more that could have been done [...]

I've always interpreted that line in Absolution as genuine - I do think there's a tendency to take the concept that it was 'too little too late' and dismiss it from there, but you could argue the same for 'Two Households' and 'Bare', if you wanted to.

*The actuality of Claire's growth being its own conversation, of course.

I know this is a topic that does require a lot of nuance, and I wouldn't claim my interpretation as more valid than any other ; I have never been religious, so I fully acknowledge that I may be missing some of the wider context from living in that environment that would inform a different conclusion.