Hi rsodre, thanks for writing us.
The Cinema 4D SDK has it's own structure which actually needs that both the plugins and the frameworks folder share the same parent folder and this is what the SDK toolset (sourceprocessor and projecttool) expects to work with. Any change to this structure may lead to unexpected behaviors and is highly discouraged.
Using the workaround you pointed out in the projectdefinition.txt is not expected to work as you've already checked.
On the contrary using symbolic links seems to work, but again this is not officially supported.
For the sake of completeness the ln command I used is
ln -s <path to frameworks> <path to plugins>/../.
and I succeeded to compile all the shipped plugins under macOS 10.13.6 with Xcode 9.4.1
Cheers, Riccardo