What are the upsides? You only listed a few things that you 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 the parts, 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. Even if you're not building custom PCs yourself, the availability of all these individual components is putting an intrinsic check on what all-in-one manufacturers can reasonably charge you.