I get a steady stream of curious flight instructors asking about it when they can't get numbers to tie up when they do the arithmetic. Of course, they must use CAS - are those stall speeds in CAS or IAS? When the manufacturer does the calculations do they use the stall speed at the same CG published in the POH or not - some manufacturers publish stall speeds for both fore and aft CG positions.
There are several reasons why a manufacturer may state a higher Va than Vs.sqrt(n). One is that they are allowing for future growth of that model so just do the certification once at the anticipated higher weight - as you saw, Va is only used to get control surface and tail loads, nothing to do with stresses in the wing. When an engineer first specifies Va it is before the prototype has flown so the stall speed is only estimated and perhaps the engineer builds in a buffer. Perhaps the actual stall speed is less than originally estimated. The structural engineering certification paperwork is largely done, they're not going to revise Va and delay the FAA's review if they don't have to.