It applies 100 %........If in the judgment of the umpire, the action ( running down and yelling GO,GO,GO) was an attempt to induce a balk, regardless of what the coach is saying.....the penalty would apply and a balk if so induced would be nulified.....
This is where you have to be sure of your judgment before you call this......This is an unsportsmanlike trick used to cause a balk and only works on inexperienced umpires. I have stopped this type of gamesmanship before.......It takes judgment of intent and only the umpires opinion matters...
And then you would most often have a real quarrel on your hands as that 3rd base coach is going to say "I wasnt yelling at the pitcher, I was yelling at my player ......Then you just have to remind them that the rule is clear that no person connected with a team shall commit any act or make "any" remark that is designed to cause a balk.......
If this is HS varsity, I expect the coach to know the NFHS rules, so I would negate the balk and eject the coach......
If this was in some summer youth rec league and if the pitcher did not balk......after it happended I would call time, call the coach down the line and let him know that he can be ejected for this if he causes the pitcher to balk....most times thats enough to put an end to this type of behavior since the coach knows you are on to the trick.....
To be honest these are the game management things that only experience brings...younger umpires get caught up in these sort of things all the time.....
hope this helps.......