There is no protest in OBR although some leagues using OBR might have added it. I don't know of any OBR guidance other than what we see is allowed as pitchers take the rubber. Basically it would be you know it when you see it. This pitcher was correctly called for a balk. He also had a "start stop" step with his free foot as he got comfortable that we wouldn't call even though he was touching his plate. But you have segued to a more nuanced issue than the OP which clearly had a pitcher near the rubber and not attempting yet to get comfortable.
For FED you have to be aware of some caseplay wording but I'll just quote this from the BRD: "IN FED, PITCHING RESTRICTIONS BEGIN WHEN THE PITCHER INTENTIONALLY CONTACTS THE PITCHER"S PLATE. POE 1987, 1988, 1989, 1997, 1998, 2008, 2009."
For all codes, think about when you would point the ball live. That would be when the pitcher is engaged.
I think he just got a generic pic from the net and is only trying to show the position of F1 in relation to the rubber. But why do you assume a LL mound?
I pulled up about 20 MLB videos of R1 with out at 2B. A little more than half had U2 outside. The distance from the grass varied some. Based on positioning I would say they all would be subject to UI but with more time to react. It looks like they don't go out on fly balls as that would have crews to have two sets of mechanics.
Other 60' orgs seem to keep the BU inside. 2man BUs do shade their B further back. I thought softball and LL have them outside for watching leaving the base.
Added some notes in your text but as regards this: "I keep hearing umpires say , yes its live here, and we offense chooses. I have had umpires stop me from calling time and taking care of the situation saying "they get to choose". but I do not see there is any scenerio ... where there is a choice? please correct me if im wrong."
There is an esoteric scenario regarding the doctoring the ball penalty where you can find the word "choice". Otherwise there is no choice in the OBR/NCAA balk rule. There are guys who dress as umpires who find it hard to understand what you understand correctly and revert to using "coach choice."
I think you would have to do your own research. Most of us amateurs would not care to put much effort into MLB's changing rules/interps regarding pitch clock. If it relates to an MLB happening Jomboy or CCS will cover it.
Batter became a runner on ball four. Runners, performing as normal, cannot be called out for interference with a throw unless you judge intent which doesn't seem the case in your OP.
NFHS use of the word "passes" generates what we call "string theory". In NFHS with fielders playing in a runner hit by a batted ball "passing" a string between fielders would not be out. They have some caseplays that confirm how they call it.