Yes.
The most I've ever replaced all at once is the CPU/mobo/RAM trifecta. But even when I do that, I still kept the same storage, case, GPU, PSU, mouse/keyboard, etc.
But otherwise, upgrades are piecemeal. New storage when my current storage is full or I want to upgrade to a new technology. New GPU when I feel like my current one is holding me back. New mouse or keyboard when my current one starts failing. The CPU/mobo/RAM trifecta when the performance gains make it worthwhile, which at this point is about every 5 years.
I'm not sure why this is hard to believe.
I guess most would probably assume at least one epic refresh where there wasn't really anything carried across except maybe the parking spot on your desk. And since the 486 era, most probably expect your desk and/or physical site changed too.
There were so many potential PC era boundaries like case and motherboard form factors, external peripheral buses, HDD controller types, expansion card buses, cooling and PSU demands, socket/RAM formats, display types, and display connection types, ...
So many opportunities to think, "this seems like a time for a clean slate." If for no other reason than to bring up the new computer and have the old continue in transition or as some kind of spare, backup, or hand-me-down.
Only one change really from AT/Baby AT to ATX. We've been on ATX now for 30 years. I could grab an A-Bit BH6 motherboard from 1998 and put it in my modern Hyte Y60 case if I wanted to.
> external peripheral buses
Since we're talking starting from 486 era, that only means going from PS/2 to USB for keyboard/mouse, parallel port for your printer, maybe serial port for a modem. During the transition period, adapters were cheap and common.
> HDD controller types, [..], display connection types.
I don't know about the ESDI to IDE transition, but I know from IDE/PATA to SATA there was a period where motherboards had both. During the transition from VGA to DVI, then DVI to DisplayPort, GPUs had both.
> cooling and PSU demands
If you overbuy on the PSU a little, you can get a ton of futureproofing. CPUs came with stock coolers until just a few years ago.
> socket/RAM formats
Which is why the CPU/mobo/RAM upgrade was typically done as a trifecta.
> So many opportunities to think, "this seems like a time for a clean slate."
Never felt the need. As mentioned above, there was frequently a transition period for when hardware supported both old and new tech.
But it would have been much cooler if you were still on the 486 era case :D
ESDI and ST-506 MFM/RLL before it lived in universe of dedicated HDD interface cards.
The buses I was thinking of included ISA, EISA, VLB, PCI, PCIe. Yes there were ways to carry some things across since motherboards often had a couple bus types at once. But in my experience, the older peripheral cards often just got retired as they became either obsolete concepts or totally integrated in the next motherboard. I.e. you once commonly had serial port and parallel port expansion cards, game controller cards, sound cards, disk controller cards, and basic 2D graphics cards.
Cases also got smaller because the motherboards needed less space, people needed fewer expansion cards, and also because people needed fewer and fewer "drive bays". In the early days, you saw both 5.25" and 3.5" floppy drives, CD-ROM drives, big chunky HDDs, and possibly other weird removable media drives. Now you can easily have a capable corporate-style PC with no expansion cards, and no drives other than the M.2 stuck into the motherboard.
On the external side, I can think of PS/2, serial, parallel, USB, external SCSI, Firewire, e-SATA. Some of these coexisted with USB until it became high speed enough to subsume them. With graphics there was VGA, composite video, DVI, DisplayPort. Sound had 3.5mm, coax, toslink, coax digital. Communications commonly had POTS modem, coax ethernet, twisted pair ethernet. Somewhat esoteric were WiFi and bluetooth adapters. These could be on dedicated expansion cards, integrated into sound/graphics/comms cards, or integrated into the motherboard.
There were also weird expansion cards that paired with a particular external device, like a scanner or Hercules monochrome monitor. And more unusual cards like video-capture and digital TV or radio tuners.
The PSU issue wasn't just overall wattage but different set or balance of voltage rails and kinds of internal connectors needed for powered components. And shifts like standby power/soft-off behaviors.
I also recall AT to ATX and later uATX. Earlier motherboards were massive with socketed DRAM and SRAM chips and lots of simpler logic chips all over. They just kept shrinking as everything got more highly integrated. If you ever got a surplus Dell you might have encountered BTX too, which was like the left-handed universe.
I also had a phase with two uATX cases and almost had a "two space garbage collection" upgrade cycle, shifting parts in, between them, and out. One was my desktop PC and the other a "media PC" attached to TV and home stereo.
Some folks like me had a phase of trying to accelerate the down-sizing, abandoning our ATX/uATX for things like the Shuttle XPC mini/bookshelf computer formats. This meant more incompatible chassis, motherboard, and PSU formats. For me, a computer after 2000 was case/PSU + mobo/CPU/RAM + disk. The disk was either a single HDD/SSD or small software RAID array. At one time, we needed multiple disks for capacity, but now it can just be one or two M.2 drives on the motherboard and no disk bays at all.
This also leads to periodically thinking just a laptop will suffice, and then that becomes another thing that sees little upgrade and carry forward over longer time periods...
Usually for aesthetics though. Better airflow was secondary until more recently.