One think I like about homebuilt desktop PCs is not just raw power, but also the large amount of options regarding ports, drives and extension cards. In laptops there is potability to consider, not so much with desktops.
For example, my tower has 3 5.25" front facing bays used. One for DVD, one HDD rack, and a multi-card reader with USB3 ports. Plus front panel jack connectors for headphone and microphones, and extra USB. Inside is a 3.5" mechanical hard drive in addition to the SSD, and an extra USB3 controller (for the Oculus Rift, which is quite finicky). It doesn't fit in a downsized case, and even finding a case with more than 2 front-facing 5.25" drives is hard enough these days.
Do I use them all every day? Obviously not, I'm not sure I even opened the optical drive this year, and it is not a feature I want on my laptop. But if I need to read or burn a CD or DVD, I know I have a computer that is ready to do that.
For me, small form factor PC still have a place in the living room. To watch movies, surf the web, play games, etc... Kind of like a modern game console, but more open. But for my desktop, I like to have everything at hand, even if it costs a bit in terms of clean look and makes cable management tricky.