...what I would really like to learn is the ability to track a card in the deck even while using genuine cuts and shuffles. So that if I know where a card is in the deck, I can perform some actual shuffles, and cuts, and still realize how many cards away it is from the top of the deck....
I don't know of any magician who can do this with 100% accuracy. Sounds to me like what are striving for is a pipe dream.
It's not that this sort of thing can't be done. Rather, your parameters are excluding the methods typically used to acheive it.
As you suggest, tracking a card and controlling a card are two different things; your topic heading, in fact, contradicts what you actually want to do.
Controlling a card -- i.e., exerting "perfect control" over a card's position in the deck -- requires you to use false shuffles and cuts, "false" in the sense that you are negating the randomization associated with a true shuffle or cut. One or more cards can be placed at any position in the deck via false shuffles which appear to be normal and random. That's how it's done, but you don't want to do that.
Tracking a card -- i.e., being able to instantly determine the position of a single card in the deck after it has been shuffled and cut fairly -- is typically done via a combination of estimation and physically marking/altering a card. If you are using roughing fluid or diachylon or some other substance that must be applied in advance, you must also be able to force that card. If you want the spectator to have a free selection, then you must mark the card after the selection, such as with a nail nick. Once the card is given a mark which can be seen from the side of the deck, you can then estimate its position. Of course, there's a reason why it's called an "estimation;" you will not always be right, especially if you are dealing with an older deck. In a nutshell, tracking a card during free shuffles and cuts requires physically altering at least one card in the deck, but you don't want to do that.
So... what's left? I have no idea, and I've been doing this for 35 years. I really don't know why you are setting the conditions you are setting. Is it because you want the spectator to do all the card handling? That's the only reason I can see off the top of my head. If you're going to be the one handling the cards, you are better off learning false shuffles and cuts that allow for precise card positioning. You can do that with any deck and don't have to mark the cards in any way.
Show a layperson a performance video of Bill Malone doing "Sam the Bellhop" and see if he/she thinks the deck is being shuffled and cut randomly and fairly.