I know, it's probably a bit late now, but you can clean install from the upgrade media. The setup program merely asks you to insert the installation floppy or CD into the computer to verify that you actually own an older qualifying operating system.
To clean-install Windows 98 using the Upgrade version, it would accept either 3.1x or 95 installation media. After the verification, it'll proceed to work exactly like the fully-purchased product version, no cruft from an older OS (since the older OS was never installed in the first place).
I know they continued doing this at least up until Windows Vista and 7. Helpful especially since Windows 2000 was a qualifying operating system for Vista upgrade, but a direct upgrade wasn't possible from 2000; it could directly upgrade from XP, though. Windows 7 would restrict the qualifying OSes to XP and Vista, and only allow direct upgrades from Vista. (Never tried newer versions of Windows, can't say what 8/10/11 do, but I have little reason to believe the practice has changed.)