(Sorry, I edited my response a bit before I sent it, and didn't change "latter" to "former", hah)
It's undeniable that some serialization formats have native support for deduplication where others do not. Hence the example of binary plist I gave. JSON does not have native support for this. Building deduplication on top of it requires building (or reusing) a scheme on top of JSON for doing so. An equivalent data structure encoded with and without deduplication/reference support would be entirely different things, and the deduplicated one would not be readable unless the caller knows the deduplication scheme. In contrast, equivalent binary plists encoded with and without deduplication are readable by anyone.
Furthermore, suppose you do build/reuse a deduplication scheme on top of JSON, then decide you want to switch over straight to binary plist. You've now built custom deduplication on top of a format that already supports native deduplication! (Foundation keyed archives encoded in binary plist are a manifestation of this.)
I'm not saying the concept of text-based reference support isn't useful (Apple platforms have used and continue to use XML plist keyed archives), but I think it's generally more optimal to reach for formats that natively support this need, if possible.
Anyway, I don't want to dwell on this entirely too much here, because I know it's not your main point, but I think we'd be better off exploring options in which features like de-duplication are composed on top of the core encoder/decoders instead of something built in to them, so things like decoding "normal" JSON aren't burdened with irrelevant complexity. Whether that's through additional macro support or composable types, I can't say right now. (I'm vaguely thinking, like, build the deduplicated structure in memory, then pass that to the JSON encoder.)
My larger point was that some research is needed into serialization limitations that have been discussed in the past. I only knew about that thread because I participated, but there are probably others.
I've certainly done a fair bit of this research, but I will always welcome someone bringing up a concern they think isn't being properly addressed. Calling those up is one of the primary points of this thread.