Are you having him weld those two parts together? If so, you really should jig up any mounting sections as its going to be hard to get it right. Even better if you can bring the bike in and mount the header and the lower section so they line up with the mounting points on the bike. I forsee you struggling to get it to line up unless there is a lot of slop in the mounting hardware or you are okay with slotting/drilling out mounting holes. If the muffler needs to be in a specific location, misalignments here can make it worse as well.
If you can't bring the bike in or create a jig, I would have them tack weld it first so you can take it home to test fit it. If it fits, he can weld the full seam, but if not, he cuts the weld makes and adjustment and you try it again. Make sure it fits tack welded together before he fully welds the seam.
If you can't bring the bike in or create a jig, I would have them tack weld it first so you can take it home to test fit it. If it fits, he can weld the full seam, but if not, he cuts the weld makes and adjustment and you try it again. Make sure it fits tack welded together before he fully welds the seam.