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.)
Vista didn't quite allow that, but it did have a dumb workaround: you could still install Vista, but it wouldn't activate until you proved that you owned an older product.
Well, from the unactivated Vista, you can run Vista setup, and "upgrade" on top of itself. That was enough for the OS to flag itself as being an upgraded install, and you could activate from that point.
It was that along with the original lasting so long that made me realize that Microsoft didn't care much about customers pirating, they didn't want manufacturers pirating.
That does ring a bell but I don't _think_ Win98 accepted Win3.11 floppies as valid media (or at least did not accept mine, which I am not sure were 'originals') and my Win95 disc was also an upgrade version.
I do remember playing similar shenanigans just a couple of years ago when I bought a laptop without Windows and I did not know that the Windows licence that came with my old laptop was bound to that machine...
I had a random Windows 8 key lying around and through a bit of wrestling (which I should have probably documented...) I was able to use that to install a new copy of Win10 on my laptop (which should be upgradable to Win11).
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.)