Technically, it warps the housing. If you talk to an axle builder, they'll tell you that all brackets should be welded before the housing ends are attached because the tubes warp.
I don't worry about it though. This rear was slightly warped when I got it in original form, and this is the second time I welded the 4 seats on bottom and the tabs on top. This is the same axle that you see in the inboard leaf spring tech page, so it's been welded on all over the place a number of times. It's still only warped about the same as it was when I got it, and I never had any troubles with it.
And if you're going to use the original spring seats, the only welding required is the upper link tabs - the second set of seats does not have to be welded. I weld those top tabs on assembled rears all the time without a problem. This rear just had brackets all over the place, so I decided to clean it all right off and start from scratch.