This thread and linked ones cover this subject. [1]

TLDR: DOS 7.1 from Windows 98 SE is generally preferred (support for FAT32 and partitions bigger than 2GB) as the very few things that don't work out of the box are easily patchable to work or have workarounds/alternatives, even Window 3.x [2].

[1]
DOS 6.22 and Windows 98 SE Multi Install

[2]
Making Windows 3.11 work in DOS7.10 (patches inside)

It depends a bit on how retro your 'retro' is. For anything 386 onward, I'd go with the above suggestion for MSDOS 7.1 from Win98SE or potentially FreeDOS (or just use some FreeDOS tools with MSDOS 7.1). However if you want to play with XT-level stuff I'd suggest PCDOS 7.1 instead, as it offers similar features but a 10k lower memory footprint, which might well matter if very constrained. I also think it feels faster, which might wel be due to that lower footprint and glacially slow I/O on those systems. Also, the 'E' editor is simply amazing, it was love at first sight when I ran it 😉

I prefer Win98se MS DOS 7.1 for >= 386 builds, but it won’t boot on a 286 or older. It has 386 instructions. For Xt’s and 286’s, I usually try to use something period correct for the hardware.

I am all over the place, DOS 3.3 on my turbo XT portable for "orfentissitty innit" ... DOS 6.2 and 6.22 randomly according to what disk I grabbed... DOS 5.0 on one system, I guess so I can do that condescending mmhmmm that wine experts do when an amateur tells them that a $15,000 a bottle vintage tastes like supermarket house white with a spoonful each of honey and vinegar in it, when ppl remind me of the improvements in 6.22 or 7.1

But yah, pretty much anything that will boot from a CD will boot 98 so go for max utility.

While having the OS install files on another partition is definitely a good idea you still want to use the same version boot disk as your going to install, this way you can simply go format c: /s (or sys c:) to make the drive bootable again.

but as as a general utility boot disk, Win98 is backwards compatible but also gives supports for LFN and what darry said above.
FreeDos may be even better, but I've never used it.

If the PC in question can natively boot from CDs then I would assume Win98SE is the system that would suit it best.

That being said I don't quite understand why you need to have only one? I like floppies (but I understand not everyone does) and I have self-made boot/rescue disks for DOS 3.31, DOS 5.0a, DOS 6.22, Win95 OSR2 and Win98SE. If I need anything else I can always make another floopy and/or reimage it from a sector copy I've made before. If you stick to just one floppy you can perhaps partition and format the HDD but you can't transfer the system. It's easier to make sure you've made a DOS compatible partition if you don't use FAT32 capable tools. And so on.