It's been a while since I've been active in the research community, and it's possible that this is a controversial opinion, but I suspect it's still true that the Schema Theorem is not really used that much to inform our modern understanding of GAs. That doesn't mean that it's not true or useful as a tool to think about the dynamics, but I think we struggle to use it to answer interesting questions, so it's just not all that relevant today. The fact that it is independent of problem instance is a pretty large limitation, because GAs are great on some problems and terrible on some problems, so if your explanatory tool doesn't have "problem" as a variable in the model, you're obviously missing something really important. Specifically, what it really describes is the dynamics of the population over time, whether or not those dynamics are performing anything we'd describe as a useful search. It's similar to the idea of a hill-climber that thinks it's doing great because it's climbing the tiny hill that's nearby and completely missing the much higher peak over there. All you have is a model of how the climbing looks, and not a model of what climbing that particular peak means in the broader sense of how well you're doing on that optimization problem.
That said, you can kind of look at Holland's schema theorem as two things. It's (1) a qualitative statement that GAs work by recombining short pieces of solutions into longer components in a way that progressively improves overall fitness, and (2) a quantitative and precise inequality that puts bounds on the probabilities for the mechanisms that are responsible for that progressive improvement. The first part of that is pretty much a given to be true for any GA that'd we'd recognize as a GA. It's just the kind of statement that you squint a little and go, "Yeah, that seems obviously true I guess". The second part only works on the "canonical GA", because the computation of the probabilities assumes a specific structure and set of operators.
If you want a similar schema theorem for some custom representation and set of operators, there's no real alternative to just trying to do the same math Holland did. What does a "building block" look like in my non-binary GA? What is the probability that my crossover operator disrupts such a building block? What is the probability that it creates such a block? Same for the mutation operator. Coming up with those probabilities tends to be pretty hard to do for any complex representation, and if you do it successfully, you don't get a lot out of the effort (because that inequality is difficult to put to a pragmatic use).