To the best of my understanding, if you use the method they show on the brothers-trucks site, you shouldn't have any need to trim.
Procedure is as follows:
++Mock the patch panel on the existing metal, making a mental note of where the rusted-out areas are.
++Cut through both the patch panel, and the original sheet-metal (which is rusted).
++You are left with two "loose" pieces of metal.
1-the old rusted crap
2-the new patch panel
Both should match precisely
++clamp the new panel in place and weld.
You guys would know better than me, as this is going to be my first attempt (after I practice a little of course). But the logic involved seems to make more sense to me than what you guys are proposing...I just wanted to get the "experience" factor involved in this mix.