You’re kind of missing the point. Their business is built on distinguishing themselves. Apple is famed for design. They’d be shooting themselves in the foot to make things like everyone else does, because then they’d be competing with the eleventy-billion other computers with the same capabilities and virtually identical design. When they were doing what everyone else was doing is when they almost went out of business. The period since 2000 or so, when they’ve been doing their own original designs, is when they’ve been increasingly successful. Not that hard to figure out why they aren’t following the crowd here.
Even the stuff that happens to look like your standard-model tower, like the Mac Pro, is much better designed inside and out. I mentioned this in another thread, that the case I got from Thermaltake, which got rave reviews from people who build computers as a hobby, feels cheap, flimsy, there are pretty big gaps where some of the pieces fit together, and you still have the web-of-cables problem on the inside. In contrast, I was at a buddy’s place when he upgraded his hard drives in his G5 tower. That thing is solid, has nice tight tolerances, and swapping drives was like sliding in a drawer. No cable routing, just slide it in until it clicks. Done.
If they wanted to do the same form factor as everyone else, they’d do it, and given then example of the tower they do make which follows your idea of, “the most common and effective way to build a computer,” they’d obviously do it well. They’ve chosen the form factors deliberately as a way to stand out, and it also gives people a choice they wouldn’t have otherwise. There pretty much aren’t any companies other than Sony making all-in-one designs.
What if you don’t want a box and a monitor? What if you’ve only really got space for a monitor and a keyboard at your desk? What if you want a small form factor computer? I suppose you could always buy an Asus that’s more expensive, has lower performance than a Mini on everything except for its Wi-Fi, is bigger, uglier, and look, it has a pen holder! Yeah, good design choice there.
If you think the OS is the important thing, getting hung up on design is kind of petty. Like that site I linked to earlier shows, if you compare on what you get for the price, you pay about the same or less for an Apple. Yes, if you’ve already got a screen that you want to use, you might consider the built-in screen on the iMac to be a waste. On the other hand, why not run your old screen as a second monitor? If you don’t want a Mini and you don’t think the iMac is worth buying, and you think the Mac Pro is too expensive, you do fall into a gap in their lineup.
But you do have a choice: go buy one of the several hundred other computers on the market that does match your perceived needs. Apple’s niche is successful precisely because they don’t try to be all things for all people. They do their thing and they do it well.