Weld subframe connectors loaded or unloaded?

As long as you don’t intentionally put a twist in the car by significantly loading one corner and not the others it won’t matter a lick.

There are plenty of places, and numerous build threads on this very site, where frame connectors have been welded in with the car upside down on a rotisserie. Some really high end builds have been done that way and I haven’t seen anyone say they welded their subframe connectors in on a rotisserie and haven’t been able to line up their body panels.