You can submit Glitchless runs to the Level leaderboards. We just don't separate them out, as there would be many empty boards for glitched.
To add to Ben's point, IL's have always included glitches where possible as the point of an IL is to complete the level as fast as humanly possible.
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As of today, any new submissions of S3K from the Steam version will no longer be allowed. This is due to a couple of factors but mostly being inhibited availability as SEGA delisted it when releasing Origins. Any existing runs will remain unaffected.