my $s = Scope->new( probe => $netlist )
             ->anatrace(
                 in    => [ 'System input', 'active', 1 ],
                 out_1 => [ 'Lpf bank1', 'active', 1 ],
                 out_2 => [ 'Lpf bank2', 'active', 1024 ],
                 out   => [ 'System output', 'active', 1 ],
                 bank2 => [ 'Switch pos', 'active', 1 ],
               )
             ->generate();
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In this example the arguments to anatrace really aren't mutators, they are constructors of sub-objects. They are waveforms being added to a scope display.

update
Is the problem that you perceive just with mutators, or does it also apply to sub-object constructors? Can you provide examples of acceptable method chaining, and contrast it with problematic method chaining?