> Are there systems that can boot CD-ROM interfaces that don't have USB boot capability still?
New x64 systems? Probably not. But since it still supports x86 and a whole slew of other architectures[1] still that don't always, it probably wouldn't make sense to stop.
NetBSD supposedly supports 486, I don't think you're going to have much luck with USB there.
There are some ISA USB cards with custom drivers to support them and present them as normal drives under MS-DOS. Never tried it myself, but they exist and seem to work!
Other commenter is correct, there are some late 486 boards with PCI support that would allow USB 1.0 or even 2.0 cards to be installed and used. Probably slow, but should work.
On the topic of modernizing a 486-class machine, there also exist a few with native PS/2 mouse support, and certain Matrox PCI cards have digital out, so it'd be possible to build a 486-class machine with USB 1.1, DVI/HDMI, and PS/2.
Since some Logitech wireless mice support PS/2, one could connect a 486 rig to a crisp digital LCD, use a wireless mouse, and plug in USB flash drives, sound, 10/100 network, NT 4.0, etc. -- all supported. Can make a fairly "modern" machine out of a pre-Pentium chip.
Some higher-end 486 boards[1] were made with PCI slots, so retrofitting them with an USB controller shouldn't be difficult? You'll still need a boot floppy to actually boot from an USB drive, I think?
1. https://theretroweb.com/motherboards/s/asus-pvi-486sp3
It is still easier to find cdr than floppies anyway. I can still find some in brick and mortar supermarkets. Still useful when you have an old car and want to keep the original audio system.