This is really an extended comment, but it seemed like a useful general purpose answer for people making magic within a science framework, so I've written it as an answer.
First off, in the comments I argued that there really isn't a "thing" which is a "bonded set of molecules." That's because nature doesn't have discrete states like that. There isn't "bonded" and "non-bonded." It's more accurate to look at it as a range between fully bonded and completely independent. However, there's a rather sharp transition region which we observe few molecules to be in. If we simply assume molecules never spend enough time in that state to matter, we can treat it as if there were two clear states: bonded and non-bonded. It isn't that those states exist in reality, its that it's effective to model things as though they did exist.
Which leads to the most important rule for magic systems like this: Sanderson's First Law of Magics:
An author’s ability to solve conflict with magic is DIRECTLY PROPORTIONAL to how well the reader understands said magic.
To this end, who cares if physics says that bonded vs. non-bonded is a non-real simplification of reality. Most readers have some fundamental concept of what it means to be bonded. As long as they understand it, that's all that matters.
Now if you never push the corner cases, you're set. However, let's say you do want to push the corner cases. You want to see whether you can "sync" with something that is in the process of sublimation. Now, your reader may not have enough of a fundamental understanding. Now you might need to dig deeper into the physics to analyze how "sync" should occur. Don't want to push it? Then you're golden! Sanderson's law is the key.
Now, if I may offer a suggestion which makes a lot of the rules-lawyery stuff go away: let magic operate on the "self." "Self" is a noun which does not have a precise physical meaning, but every human being out there has some concept of themselves. If you admit a concept of "self" into your magic, you gain access to a whole slew of natural easy to understand concepts which make these sorts of games easy.
For example, you primary concern is teleportation of clothing. Make the teleportation spell work upon what the individual sees as "themselves." Make it work on their mental image of who they are. Most people don't visualize themselves naked on a regular basis, so that means most people's sense of self extends to their clothes as well. Now there's no issue at all with syncing. You naturally will sync with your clothes, and that's a concept readers understand, so you don't have to dig the physics any further than that.
In theory one could abuse this by successfully visualizing something else as part of themselves (you can visualize anything). However, if you really truly feel that it is part of yourself, there are serious consequences. For example, you must protect that thing as part of your self, just like you would protect a finger or a leg. You must feel mental anguish if it is damaged. People can manipulate you simply by threatening to damage the object. If you don't have traits like these, then you didn't really treat it as part of yourself, and you wont sync it.
If you wanted to, you could also blur the line of what is "synced" and instead have degrees of being synced. You and your clothes may be highly synced. The pin you just picked up may be very low on this scale (but increasing continuously because it's within 2-3 inches of your self). Now make the rule that you can teleport anything, but it takes more energy/mana to teleport things if they aren't well synced. Teleporting with that pin might take great effort.
Now you have a very rich system. A normal person does not think of a gun as part of themselves, so they could not teleport with a gun with ease. However, a gunslinger whose life has depended on that firearm may think of it as an extension of themselves, in which case teleportation with that gun is easy peasy.
You can even bend the rules with this. Consider a Japanese warrior-monk whose family has safeguarded an heirloom katana for generations. That monk may be so synced with this heirloom that they can maintain the sync, even beyond the 2-3 inch range. They could teleport that katana right to their hand from across the room. And it won't seem overpowered because this monk has literally devoted their life to this cause.
All of this is easy because the concept of magic was allowed to operate on our mental image of ourself. There's no easy physical description of what that means, but every reader intuitively understands it.
Oh, and if you want to use it, you could consider taking advantage of the concept of Evanescent Waves/fields. This is a real life phenomena which occurs over very short distances (fractions of a wavelength) where energy which is totally reflected "leaks" out of an object. It occurs because of the same issue we started with. We think of light reflecting off the edge of a prism as reflecting off a border, but the physics of light waves doesn't recognize borders like that. When you model the full wave behavior of light, you find there must be a fuzzy region "outside" of the prism where light acts funny, just like the 2-3inch region around the self where sync occurs.
