To parallel a discussion in another area, a player need NOT have his knee, or any other body part, on the ground to be officially the 'holder' for a place kick. Obviously, unless he is David Blaine, or from another planet, and can levitate, he would have to have SOME body part on the ground to be able to hold the ball for the kick. But, no rule REQUIRES the holder to have a body part on the ground to be classified as the 'holder;' only that he be actually holding the ball on the ground and that there is a player in position to make a kick. A 'holder,' then, has the exclusive ability to be in possession of the ball with a body part other than the hand(s) or foot/feet touching the ground, and the ball remains alive.
On a scrimmage down, it matters NOT if Team A is in a scrimmage kick formation (SKF), or otherwise. The SKF has nothing to do with determining if a player is a kicker or a holder. A SKF is primarily intended to allow Team A to have exceptions to mandatory numbering, and there are some pre-snap positioning restrictions and blocking restrictions for Team B. Oh, and a DOG by Team A from a SKF also requires the clock to next start on the snap.
But, a kicker can be a kicker, and a holder can be a holder - both as defined - regardless of what formation Team A may have assumed at the snap. It only needs to be "...obvious that a scrimmage kick will be made,..." IN THEORY (but highly unlikely), during the middle of a scrimmage down, a ball carrier (from behind the NZ) could assume a posture that is obvious that he plans to kick the ball, and he is protected from running into/roughing. Same for a holder. As unlikely as it is, during the middle of a down (from behind the NZ), a BC could drop down and hold the ball on the ground and a teammate could be in a kicking posture, making them "holder" and "kicker," respectively, and 1) the ball would remain alive and 2) they both would have running into/roughing protection.
Bottom line: A) No rule requires a player to have any part of his body touching the ground to be classified as a holder. B) A scrimmage kick formation is totally unrelated to running into/roughing the kicker/holder.
There might need to be an editorial change to the definition of a holder. Currently, he must be controlling the ball "...on the ground or on a kicking tee." Hmmm. Using a tee for a field goal attempt is not permitted. OK, occasionally we see a holder for a free kick (windy conditions). But, does he have running into/roughing protection? Does he need it? Questions for somebody else to answer.
Also, the protection for the snapper applies when Team A is in a bona fide scrimmage kick formation, which means that they have no player in position to receive a hand-to-hand snap, and either one player at least 10 yards behind the NZ, or a potential holder and a potential kicker, both of whom are at least 7 yards behind the NZ, and, in all cases, “…it must be obvious that a kick will be attempted.” Again, the potential holder need not have a body part in contact with the ground, before, or while, controlling the ball on the ground. So, if the down/distance/time/score factors are appropriate, and a Team A is deemed to be in SKF, then Team B must not have anybody aligned within the frame of the snapper’s body at the snap, and the snapper is afforded his ‘delayed’ contact protection. The potential holder does not need to be on either, or both, knees, ever. Even while holding the ball for the kicker. If he can squat and hold the ball, then he is the holder. And I see nothing that would prevent the holder from controlling the ball with one foot, if he can successfully get it placed and get his foot on the top tip of the ball.
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