@Meanlucario  
I have read the series, and Lyra shows every sign of being a lovable and caring roommate who Bonbon really appreciates, to the point of them looking like an old married couple. Basically, they are showing every sign of being best friends on a similar level that they are in canon, and there is no evidence either is interested in a relationship outside of that life partnership, beyond Bonbon thinking she might want kids eventually.

@Background Pony #8392  
I think it’s more of shock that Lyra may have a boyfriend, though that’s just how I read it.

@Meanlucario
 
For whatever reason, some don’t realize this is an AU. For example, Spike has no crush on Rarity here.
 
That said, the second panel does seem like a reference at least. But it might not be.

@Background Pony #5654  
Again, if you read the series, they aren’t in a romantic relationship in it. And I’m talking about this fan-series, not the show in this case.

@raw19
 
“Beware!”

Let’s just hope that fort isn’t haunted.
 

@Meanlucario  
Well, in Canon they’re a couple, so much like Shining and Cady, you just kinda assume.

That is so precious
 
Fast forward to where they melt the fort with a water hose after they get bored

Funny Lyra funny boxes in a box!

Such a Lyra thing to do.

@Background Pony #8392  
In that case, I don’t think she ever shown any romantic interest in her in this series.

@Meanlucario
 
Second panel

@Background Pony #5654  
I don’t see what that has to do with this.

Give us a tour of your cardboard castle.

Bon Bon, it’s okay. Lyra only has eyes for you.

Boxception!

They’re minerals! Jesus, Marie!

Those boxes are for shipping, not for creating a world of pure imagination! Give them back!