Replying to my own post for future me (and other developers).
After a few days of digging and investigating, this turned out to be a bug in Xcode 15 and has been fixed in 15.3. The releases notes are below:
Fixed a bug where in a workspace with multiple projects, if a target is configured to merge the binaries of its immediate dependencies into its binary, it would not see that those dependencies were built as mergeable if they were in different projects from itself. (115400802) (FB13160508)
If you can't update to Xcode 15.3 for whatever reason there's a fiddly workaround I pieced together.
On your mergeable binary (in my example FrameworkC) ensure that the "Build mergeable library setting is set to "Release" only and is set to "No" for debug.
On the consuming framework (in my example GroupFramework) you can explicitly add the required linker options to merge the binary.
Wl, -merge_framework, FrameworkC
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@peweone Did you ever find a solution for this? I'm seeing the same issue in debug builds. The runtime can access the bundle, but the bundle path points to the Reexported binary. When I inspect the reexported binary on disk, it seems to have the resources stripped. I have embedded the framework into the main app target as suggested by @eskimo but because the bundle path isn't pointing to it, it doesn't solve the issue. It's fine in release builds