Will a sniper with squad sight on overwatch fire at targets allies can see

Actually those are the only two penalties to reaction shots I have encountered. At the exact second your character starts to fire, it is as if the enemy was standing there at that moment and told them to shoot and then subtract the aim penalty (-20 I think). In addition you can use this to your advantage and place a smoke where your character is dashing through. You will gain the defense boost if you are shot at while in the smoke.

Finally, I do know that there are bonuses you and enemies gain when moving or more specifically when dashing. When an enemy is dashing they are a moving target and have a higher defense and thus harder to hit. The combined reduction of accuracy from overwatch and dashing bonus from the enemy makes it very hard to hit reaction shots.

That specific perk basically removes all penalties to using overwatch on a sniper. It's pretty good when combined with squad sight.

This is all only in my experience however and I can't check what the enemy chances to hit are. I'd like to do some testing in multiplayer if possible.

No, it is not.

Your already promoted soldiers will be at a will disadvantage to the new soldiers you receive. If you record the will levels of your existing soldiers and then take the upgrade, you'll see that it doesn't change.

Because of this, its better off if you get this earlier in your game rather than later.