Bust that bible open read the verses to me back

Now... where do we begin? Oh, right. In the part after you're done with Naraku and get to spend the holiday with the other two.

This scene is presented in almost the same way in both languages but Jonathan's reaction seems emphasized on a specific word in the Japanese script.

"T...t-t... that's crude, Walter. I would never... such a thing like that to women..."

In either case, if this ended at Jonathan's response, it would be mostly nothing worth commenting on. Jonathan is the Law representative raised by a family that worked in the Monastery so naturally he's gonna behave in a more chaste way, correct?

But then you have Walter's posture becoming uncomfortable followed by immediately changing subjects as if he's already in the know of what Jonathan was anxious about compared to the player (thus Flynn) being rather out of loop about what was going on.

The thing is... the meaning was actually already available for the players, even prior to SMTIV's release! That is, if you accessed the official website and clicked on the interviews with the Japanese voice actors (which included in-character voice clips). All of the translations presented in this post were done by takujilvr

"I'll only tell you this because it's you, all right? Only because it's you! I'm afraid I can't bring myself to like women very much. Being raised in a household with two elder sisters and one younger made me lose any illusions about them I might've had. You're a man, so I feel much more at ease with you."

Certainly, he doesn't seem to specifically refer to anyone in this clip. It could be Flynn or probably anyone else as long as they're a male.

But there are other voice clips aside this one that point towards a more definitive interpretation.

"Enough of that "Ooh, you'll catch cold!" drivel, Jonathan, you sound like a naggy old wife. I can't abide being constricted, this chest must stay bared!"

"S-Stop pulling my hair, Walter! It won't straighten out, I got it from my mother!"

They don't have voice clips directly acknowledging anyone else, leading to the impression that Walter and Jonathan were being more marketed as a duo over their dynamic with the main character.

But the shocking reveal comes with this one:

"I'll only say this if you promise not to tell anyone! Cats, I just love 'em. When I see one outside, I can't help but crouch down and give it some pets! Wait, no. I mean, listen, I can't stand fish. And they can take it off my hands, can't they? That's why I love cats. Right."

A player that reached the part where the party gets hit by Yaso Magatsuhi's scent in Roppongi will thus connect the dots:

How one interprets the twist of this scene might change entirely with the voice clip in mind. It opens the possibility that, differently from many players' assumptions, Jonathan was acting like a feline not because he's secretly a cat lover. But, most likely, due to WALTER liking them. And he would have no way of knowing that unless Walter told him off-screen.

To summarize...

Jonathan is unable to feel attraction for girls and feels more comfortable with guys which would be inevitably an obstacle for his future considering his conservative background

Walter has phobia of fish despite what his family does for trade and has a soft spot for cats specifically because they eat them for him which would be defined as a 'weakness' to his self-reliant image

1 and 2 are each most's intimate secret and they revealed them for each other

"But how much does this add to the main plot?" Even when pushing aside subtleties from this extra material, attentive Megaten veterans would notice that the Law & Chaos representatives from SMTIV have an explicitly close bond compared to most characters of opposing sides in other titles of the mainline series.

[Jonathan was the most visibly affected by their breakup]

This extra material essentially adds more to the range of interpretation regarding their intimacy while also making them more relatable beyond their surface of Law & Chaos pieces.

On this note, moments where they "crack" their own alignments also happen briefly in-game.

They were two boys of the same age that became instant close friends however became unable to conciliate the differences emphasized by their caste system and reach the understanding of what would be the best for everyone.