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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In addition to the previous news post about extra IL variables that allow runners to submit runs that start Act 2 with glitches, shields etc from Act 1, we have decided to remove the Legacy Ruleset, to do this we have grandfathered any runs that adhered to the current ruleset and just don't meet the