It isn't a matter of waiving the requirements, it a matter of tweaking the inspection criteria to fit the purpose of the tack weld, i.e., ensure the nuts cannot back off. Essentially this application simply involves destroying the threads of the bolts so they no longer function. If the fasteners were made from 316 or 316L, no filler metal would be required. However, since they are 304 or 304L, the low ferrite could result in a cracking problem and your WPS is qualified with filler metal.
Again, this is a situation where the engineer has to give a little thought as to the amount of weld required and what visual criteria is appropriate. Welding on a threaded fastener is more than likely to produce undercut and unfilled weld craters simply because the threads are melting. Basically, if the weld isn't cracked, it should fulfill it's purpose. Even if the weld is cracked, it would do it's job, but it would give too many people the heebie-jeebies. Heck, clean the stainless fasteners in alcohol before installation and tighten them a little past snug and the galling will keep them from loosening. Smack the threads with a small cold chisel and the nut is never going to come off! You could cut the bolt flush with the nut and center punch the end of the bolt and the nut will never come off. The latter method gets my vote. Run a couple of tests to demonstrate the technique works and go for it. Welding; too many variables that causes every pin head on the job to start looking at the weld with a magnifying lens.
As for the 303 stainless, cracks are almost guaranteed due to the high sulfur content. Once again, the last method of upsetting the end of the bolt gets my vote, especially considering the diameter of the fasteners involved.
Best regards - Al