The trade-off is Alvearies are (coded) to be 10x more productive than Apiaries. Yes, frames are used/burned 5x faster, but you get 10x more products. When you put it into those terms, you get 2x the frame efficiency alveary vs. apiary.
For breeding, I almost always use Apiaries. My Metabolic frames last a lot longer as a result. 3x Metabolic in an Apiary is usually sufficient for 5% and above species. If I was doing a lot of Metallurgy with those 2% species, I'd invest in a hopped-up mutating Alveary.
When I've reached my maximum targeted bee production capacity of between 24 and 36 alvearies, I'm keeping between 1 and 2 Carpenters busy making Impregnated sticks for frames and I need a pretty good supply of Seed Oil, which highly encourages tree breeding to get more seed oil production without spamming wheat farms, unless using PfF to get the much easier creosote.