Maybe because there's so little official canon for the background characters, it gives fans the opportunity to expand every little expression, action or rare spoken word into an entire back story? Lots of fun!
Where with the mane characters, there's so much official story, there's less room for creativity.
Well, Lyra and Bonbon have been together repeatedly in multiple episodes, and bonbon has had actual speaking roles, albeit minor ones. Maybe if they'd only appeared once, there'd be less fannon?
I haven't checked, but hasn't the quills and sofas pony only been in a single episode? I just did a search in DA for "Quills and sofas" and still I got a few results. Apparently his name is Davenport! No idea where that name came from.
As for the Apple's from Ep 1. The only one I can remember reoccurring was Apple Cobbler who appeared in the background during Hearts and Hooves Day, but I don't think most people recognised her since it's been such a long time since Ep 1. There may be other background Apple's that have reappeared, but Apple Cobbler is the only one that I can remember at the moment.
It could be fan attention is in relation to amount of background time!
So repeat background ponies like Lyra, Bonbon, Derpy, Doctor Whooves, Berry Punch, etc... get repeat fan attention which then feeds back on itself?
Though there are exceptions I suppose. Fleur appeared only once, yet there's been a TON of fan work on her.
Anyway, that's just more mad theorising! Sorry for going on so long. I've got ponies on the brain