Going back to that infamous rooftop conversation between Egon and Janine waaaay back in Volume #1.
Egon told Janine that she dated people who 'shared one or more superficial characteristics' with him, and he admitted that he was jealous of Roger.
With Roger, she didn't just 'get disinterested' and 'return to aggressively flirting' with Egon, as Egon had predicted she would. She remained with Roger until HE moved away. So, there was something different about this relationship than the others she had. Presumably, this is because she was basically dating 'Egon'. It wasn't just 'any guy'. It went beyond her just trying to make Egon jealous.
Maybe she stopped aggressively flirting with IDW Egon because she is still, to an extent, getting over her relationship with 'her' Egon (Roger). A relationship which affected her on a deeper level, because it was someone she truly loved.
Going back to IDW Egon. He was jealous of Roger because he thought Roger was just 'another guy' that she'd get over and eventually go back to flirting with him.
IDW Egon now knows that Roger wasn't just another guy anymore. He'd underestimated Roger's role in Janine's affections. Roger was basically an alternate universe version of his older self. It's probably like finding out someone you love has fallen in love with your doppelganger. And he was jealous... of himself. And he knows she's not fallen back into her normal pattern of behaviour, which has probably skewed the f-ck out of his flow charts.
I think, even though Roger looked vaguely like himself and sounded like himself, it probably never really struck home with Egon until he saw EGB Egon. So, now he knows that Janine was dating someone who she really loved (a version of himself), that she's probably still upset that they are not together (because she hasn't resumed her habit of flirting with him), and that he's going to have to 'bring Roger back' in order to carry out the work he needs to do.
I don't think IDW Egon feels any animosity towards EGB Egon (he did call him an asset, after all), and I don't particularly think he is jealous of EGB Egon, either, because Janine hasn't dated him. I think he probably feels unhappy that he needs to bring EGB Egon into 'their' universe, because of the implications it has for Janine, and I think he probably realises just how much he underestimated Roger and how much Janine felt for him. Maybe there's also a small part of him that wishes he'd done things differently, and maybe that he regrets what he said on the rooftop.
I think, regardless of what Peter thought, Egon probably was of the opinion it would be best to keep them apart in case Janine would a) be upset, and b) possibly want to date the guy. Not as a Roger replacement, but as someone who she felt deeply for, and who she seems to have a natural attraction toward. As you said: what are the odds.
However, I still think that decision should have been hers.
Unfortunately for us, I don't think we'll ever find out exactly how IDW Egon feels about EGB Egon, so these are all major assumptions on my part, and obviously other people won't share the same views. But that's my take on the situation.
Also, if Tiamat is wanting to cause chaos, wouldn't it make since to put Prime Janine, prime Egon and EGB Egon on the same team?
Now, that would have been something interesting.
I think one of the problems the writer has here is that Roger’s Appearance probably was just a joke, an easter egg for the fans when they started the series. But now that they crossed the universes they cannot just ignore the fact that he is a doppelganger of some Egons. So maybe they will use it later for something of importance. But I would not be surprised if they just wanted to get it out of the way and the 68-E file was the last thing we ever hear of it.
I tend to agree with you. I think this is how they've addressed the issue, and that's the last we'll hear of it.
We're just left to speculate about the whys and hows and motives of those involved.