Think mine runs slightly better cooled with j tubes, as you're not diverting some of the air from the fan down the air tubes that feed the heating system....
I have read in the past that the entire system, including heat exchangers assists in keeping optimum head temperature, something that j tubes cant/dont do .... I do know that once you change anything these things go out the window, of course.
If you are going to run J pipes then use the industrial tin to keep the heat away from the heads - yes, VW supplied heater boxes for all markets for a reason, they don't just heat the interior but also cool the pipes under the heads.