If you're formatting the drive fresh with win98 disks, then format C:/s should be enough to make it bootable. It will have the msdos.sys and io.sys files (these are the minimum files required) but no operating system per se. Autoexec.bat is not really required as basically, it only sets language support, keyboard support, memory use etc. It should also run without the Config.sys as well. It would be a bitch to use though. If the drive is already formatted then 'sys c:' should achieve the same result.
However, if you are trying to make a multi-os disk, then unless the 'blank' drive was the first partition, I doubt it would work.