I have not bred rabbits but we do have some long-time breeders on our forum that may share their experience. I can understand that caring for many rabbits (often outdoors) as opposed to just an indoor pair has different demands altogether.
I read the article and can understand some of her points. However, there are several comments with which I'd heartily disagree.
Her beef with free-roam rabbits I disagree with. (She kept referring to this as the rabbit running "wild" & "run around like crazy") She claimed this makes them "much less friendly and affectionate" and "lessons their attachment to their owner" -- I've known and heard of plenty of affectionate, free-roam rabbits. This claim is unfounded. She also mentions the "dangers" of chewing things while free-roam but that is why one needs to bunny-proof. I could also counter with the dangers of outdoor housing as well.
Her claim that wire cages are "always cleaner than flat bottomed cages, without exception" is clearly spoken from ignorance. I've seen plenty of filthy wire-bottomed cages. Just a quick look at rabbits for sale on craig's list will show me rabbits in nasty, filthy wire cages. Any cage can be kept clean just as any cage can be dirty. She never mentions litter training either which can help keep indoor cages perfectly clean without (as she assumes) "having to scrub out a flat-bottomed cage twice per day."
She seems to also assume that all non-wire-bottom cages are plastic which they are not. I would agree that plastic bottom cages can be dangerously slippery. It's recommended to either not use such flooring or cover it with something not slippery. And I would agree that plastic would be more prone to break than wire.
I found it odd the mention of indoor cages not allowing for proper ventilation. Indoor cages often have wire sides and tops, or they have no tops at all and are very open like an exercise pen or total free-roam. The concern of ammonia build up would therefore not be a valid complaint. Nor would the idea that heatstroke is a risk in a non-wire cage (for same reasons).
She claims that broken or missing toes or toenails come from flat-bottomed cages. What?? The only torn toes I've heard of were from a rabbit getting their toenail caught in a wire-bottom cage.
And the idea that "most breeds are perfectly content without exercise outside of their cage" seems more than presumptuous. I don't think that's even worthy of comment.
For indoor pet rabbits, there is no reason, imo, to keep a rabbit confined to a wire bottomed cage. The joy of having an indoor rabbit is to be able to interact with them, and watch their fun antics, their binkies and dashes. With litter training, an enclosure or home-base can be a breeze to maintain.
There are many options for indoor enclosures and with the best interest of your rabbits in mind, "factors such as durability, safety, injury prevention, ventilation, sanitation, traction, convenience, disease prevention, and preference of the rabbit," mean that wire-bottom cages would never be my top choice.