"Given that some of these powerful set theoretic axioms are independent from each other, I'm not sure whether ZFC+CH could have a different idea about BB(8000) than ZFC+notCH would."
It can not. The TMs can only be affected by things that affect them at a finite level. To put it another way that may be easier to see, for them to have a different idea about a given BB number, there must be two otherwise identical machines facing their decision about what state to transfer into, but the one armed with the CH must choose one state and one without it must choose another. (There must always be some such first state, even if it is the very first transition.) There's nowhere to encode that inside a TM state transition table.
That is the "outside" mechanics of a TM, which are fully defined by the problem itself. The "inner" mechanics of a TM, where we talk about what the machine is "really doing", may have such effects, but that's a bit more mundane. And not even necessarily relevant; while you may have two machines, one with ZFC+CH and one with ZFC without CH, they're both going to be hammered by a machine doing "something" that definitely isn't just running a clearly-defined axiomatic system over propositions, but something "mixed up" beyond all human understanding.
What can affect the BB number is oracles. This is also in some sense "why" oracles are defined as essentially function calls that TMs can make with a sort of equivalent of a system call operation that user space code can use to invoke a kernel's functionality... you can easily encode that into a single finite state transfer. BB relative to an external oracle can be (and is) different than conventional BB. However, while the numbers are larger... much, much, much (etc.) larger... I think in some sense it's also less mathematically interesting and returns to just being "yet another large number generator"; BB is interesting precisely as the boundary between computability and non-computability, and BB+oracle is just straight-up uncomputable. But that's not that interesting, really; there's an infinite number of already-uncomputable functions anyhow.