Hard to say what will work better, a copper seal or something, or the glass fibre wrap around the pipe and all tightened up for practically no fretting space left. The standard nut will sit on whatever is the proudest spot on the hammered flange, so this will be one place for fretting and wear. So not a precise fit of nut on the flange. Yes, with flange sitting on recess in alu head same story , will eat into it in case when some fretting is not prevented by glass fibre. A steel shim could be added for protection instead of soft copper seal. But then, when the flange has formed a shape into the head recess it will sit quite well, plus glass fibres compressed it might last centuries. Only a test will show what´s the easiest way to fix the pipes on head with minimal troubles . I am thinking about the BMW chamfered rings for fixing pipes, worked great for more than 50 years on my 69 S . The finned ex nut could get the job as one of the rings, a 45 chamfer turned on the front face, so then only the corresponding slotted chamfer ring is required to clamp the pipe onto the head, sealing was always sufficient on BMs , so worth a try. No need to hammer a flange onto a new pipe, you will never achieve good alignment for head recess or ex nut face. So instead I would try softer material that squeezes as needed into all free space until quite solid joint - or so I guess . . .
Vic