Sure; eventually practically every system used 5 1/4" diskettes: CP/M, MSDOS, Apple, CBM, R-S, etc. although almost everybody had their own format and even the diskettes themselves were not all the same (Single/double/quad density, single/double sided, soft/hard sectored (10/16).
You have to remember that S-100 is only a specification for the bus that the cards plug into, and it doesn't say anything about the CPU, operating system, disk size/format, etc.
CP/M is also just a more or less standard interface between a program and the hardware, which could have any kind of CPU, diskette or hard disk (or neither), and any kind of display/console (local or remote terminal, memory-mapped, text or graphics, colour/mono, etc.)
So, both S-100 and CP/M don't really specify the actual system or what software will run on it, although unless it's all high level, the software would have to match the CPU.
Although the majority of S-100 boxes probably did run 8080 or Z80 CP/M with 8" or 5 1/4" disks, there were S-100 systems using 8086/8088s (PC), 6502 (Apple/PET/OSI), 680x0 (Motorola) etc., with various floppy and hard disks, controllers, monitors, etc. etc. Sometimes you could mix and match cards from different systems but often there were small or large compatibility issues.
DOS just stands for Disk Operating System BTW and not *necessarily* MS- or PC-DOS, at least not in those days.
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