A "bootable CD" is a CD containing its own (somehow restricted) operating system into which you boot.
So, it doesn't really matter if it was created under Windows XP or other OS - you boot into whatever is on the CD (not on the disk of your computer).
Whether the tools (on the CD) work with attached Windows 98/2000 systems... that's an unrelated question. Some of them will, some of them maybe won't... I guess you'd have to be more specific.