That charge pipe doesn't look right. It looks like the 2 or 2.25" end was chopped to make it sit lower for what purpose I can't tell, maybe the blow off valve/hood clearance, thus the bolt interference. If you look at the charge tube end there is a thin bare aluminum witness line on the edge. A powder coated charge tube will have overspray back into the inside and all edges will be painted, the OP can confirm this.
How 2J weld quality get's brought into this no idea as those pipes are painted. The 2J aluminum weld quality on mine looks good, mostly full penetration and more or less flat welds with no pinhole or evidence of burn-thru. Could be better but if it passes a pressure test and doesn't crack I'm good with it for what they are being used for.