After more thought, without taking a team time-out, there is another way for Team A to avoid illegal formation fouls related to SKFs, even if one or more players take incorrect initial positions. As Shaw makes clear in Play Situation 1 of the bulletin, "Scrimmage Kick - Numbering Exceptions, Quick Reference yada yada" (issued a few days ago), the "2x2" players don't become 'exceptions' until the snapper takes his position. So, simple. Just have the snapper take a position, laterally, where he would want to be to address the ball, but stop and hold one yard behind the NZ. Then, let the rest of the team move to their positions. Once Team A is satisfied that everyone else is where they need to be, then the snapper can move forward and take (establish) his position. That's when the "2x2" players get locked in. Following that, I would certainly allow the "2x2" players to adjust their feet slightly. But they can't trade places with another lineman (in the tackle box, or otherwise), or move into the backfield.
It is certainly physically possible for there to be more than two linemen between the snapper and the the edge of the tackle box, especially considering the rules allow a player to be 'touching' the tackle box to be considered 'inside' the box at the snap. (Note that this is true for any scrimmage formation, not just a SKF.) For a SKF, if the "2x2" get established and there is another (maybe more?) player(s) outside of the "2x2" on one (or both) side(s), the widest player (to each side) would be, by rule, the end (as defined) on that side, and, if he is wearing an eligible jersey number, then he would be eligible. (Yeah, this rule reinforces the fact that the minimum number of Team A players required for a scrimmage down is five.)
If this is a SKF, by definition, then the "2x2" guys are ineligible, regardless of jersey numbers. But, all elements of a SKF must be present: one player (potential punter) at least 10-yards behind the NZ, or a potential kicker with a potential holder, both, at least 7-yards behind the NZ and in position to make a place kick, and IT MUST BE OBVIOUS THAT A KICK WILL BE ATTEMPTED. Those last 9 words are critical, and mean not only down and distance, but time and score as well. If the formation meets this criteria, then Team A does not have to have ANY players wearing numbers 50-79, but MUST have two adjacent linemen on EACH side of snapper and within the TB, at the snap. Two is all they need on each side, but they are ineligible, even if the outside guys are, by rule, ends, and wearing eligible numbers.
On the bold assumption that I am reading, and interpreting, things correctly, it would seem that coaches should be 'coached' on this preventive measure for SKFs and numbering exceptions.