Somehow I doubt shortening the wires by a bit and shielding the amp does make a difference...
At first on my Core II, I added the amp externally to the console (right out of the console, a few cm after the connector), here's the thread with photos
http://www.pcenginefx.com/forums/index.php?topic=9379.0 So no interference from digital signals coming from the PCE board there...
I still had the same intensity jailbars like on other consoles that had the amp internally.
After some time that i managed to make the amp smaller I remoded the Core II and installed the amp inside it. No change as far as jailbars go, exactly the same jailbars.
The jailbars were subtle without the mod steve because you were getting picture through composite (or worse through RF). Composite smooths the picture making the JB less visible. RGB mod makes them more clearly visible and not nesesarily because an amp "adds" more of them.
My jailbars are hardly visible too, I make comparissons on the initial gaming screen of the Keith Courage game in which the jailbars are more easily to be spoted due to the light blue color of the sky but on any other game only a trained eye can locate them, they are almost invisible but never completely gone.
Don't get me wrong, the theoreticly right way to do it is to avoid interferences by shortening cables and shielding the amp but practicly these two may make no difference. At least I haven't seen any and I've made many trials with the RGB thing.
I have even connected the RGB signals without any amp (bad colours) and noticed that the jailbars were exactly the same (with or without it).
Thats the reason I'm positive that the secret of completely removing the jailbars is doing something to the 6260 chip (like shielding it).
Actually on the Turbo Grafx-16 there is a shielded chip by factory but im not sure its the 6260, it probably is... (picture found on the internet)