Well, surprise surprise:  Got an email tonight and they have reversed course and have now approved the RMA. 
Got my shipping label and EVGA is going to replace it.  
Seems someone agreed that there's really no way you could damage just one pin without affecting the ones around it. 
So I have to say I'm pleased with EVGA!   

Update:  New board came in today.  I videoed myself unboxing it "just in case", lol.
 
I'm typing this on PC that it's in.   Seems to be working, and all 4 memory sticks are recognized.   I just put it right back in place where the old board was, didn't have to reload Windows or anything.   Very happy with EVGA. 
 
I do have one issue, and this was the case with the old one as well and I thought maybe the missing pin might have been the problem, but evidently now:
When I boot up....I see the "X299" splash screen, hear a couple of beeps, and it says "insert disc with operating system" or something like that. 
And "press any key to continue", but that just goes on forever.   So you reboot, go into bios.....and don't change a thing.  Just "save settings and exit", and it'll go right into Windows.    But if you cut it off or reboot....you have to go into bios and "save settings and exit" every time. 
 
I didn't try and figure it out much with the first board, since I knew it had an issue, but since this one does the same thing, I guess I need to track this issue down.   It still works perfectly once you do that and it goes into Windows....but it's a bit of a pain.   
Any ideas? 

arestavo
Wonky problems like that tend to point to a dying CMOS battery (part number CR2032 if I remember correctly).

I feel you are right on target (and yes it is CR2032).

Pacfanweb
Seems odd that I would have 2 different, theoretically brand new motherboards with a dying battery.
No way to tell other than just replacing it, I suppose?

Low probability but not completely unlikely. HWInfo64 -might- be able to tell you battery voltage but I don't know how reliable that is. However, if it walks like a duck ... it is worth replacing before you build whole system around it.