The case for ending judicial or presidential appointment filibusters is because the Constitution specifically set up a process of executive/legislative coordination that preceded the adoption of any housekeeping rules by the Senate.
The filibuster does NOT appear in the constitution.
The appointment process does.
That "Each House may determine the Rules of its Proceedings" appears in the Constitution.
And the Constitution does not proscribe or prescribe the rules for the senate. The filibuster is very very old, going back to the beginning of the republic although the term was not used until the mid-19th century.