Thanks for reporting this! From looking at the code, I don’t think the problem is specific to scenes with takes. It looks like the dependency list is simply ignored when creating the job submission files. If that is the case, this will be a quick fix.
I’ve attached an updated C4D submitter that should fix the dependency problem. Just unzip to \your\repository\submission\Cinema4D\Main and overwrite the original. Then restart C4D to test the new script.