There are upsides here as well! I think of things like the NUC or Mac Mini - ATX is from 1995, I'm hopeful computers will become nicer things as we trend away from the bucket-o-parts model.
I'm very excited about the Steam Machine for the reasons you mention - I want to buy a system, not a loose collection of parts that kind-of-sort-of implement some standard to the point that they probably work together.
What are the upsides? You just listed a few things that you subjectively like, but not why they should take over all parts of the PC market. The only factor I can think of is size, but those small all-in-one computers are already widely available now without the need to hollow out the custom PC market.
There's nothing wrong with ATX or having interchangeable components. An established standard means that small companies can start manufacturing components more easily and provide more competition. If you turn PCs into prepackaged proprietary monoliths, expect even fewer players on the market than we have now, in addition to a complete lack of repairability and upgradability. When you can't pick and choose, you let the manufacturer dictate what you're allowed to buy in what bundles, what spare parts they may sell to you (if any) and what prices you will pay for any of these things.