This might be due to the presence of floating numbers in fep-8b32.feature document. Some JCS libraries don’t handle those correctly. Which one do you use?
A similar concern was raised by @helge in another thread: Use cases of fep-8b32: Object Integrity Proofs - #10 by helge. Several solutions were proposed - embeddedObjects, re-defining object as @json, etc.
Later, I opened an issue in w3c/vc-di-eddsa bug tracker - eddsa-jcs-2022 and nested documents · Issue #81 · w3c/vc-di-eddsa · GitHub. They said it is fine to embed a signed object and I didn’t ask any more questions.
If I understand the question correctly, this problem also arises in client-to-server context. An object published by a client can be parsed differently by the originating and receiving servers due to JSON-LD/JSON differences. This could cause security issues, and I have lately come to the conclusion that JSON-LD and JSON cannot coexist in the same network.