I do not believe that any additional information or regular notes about entry lines is transmitting with the return.

I can not provide any definitive source, but my understanding for several years is if you want anything additional transmitted you must use the Preparer Notes. In the 1040 module if you hit F6 to bring up the forms directory and in the upper right scroll down to MISCELLANEOUS, Part ll Miscellaneous Statements and Reports # 3 title is "Statement for Additional Information for Efiled Returns", which may imply that this is where you need to put information you want transmitted with the return.

There are no statement in the other modules that I have been able to find which provides such a hint about what transmits and what does not for those (1041, 1065, 1120S, 1120)

There is no reason at all to believe that just because you called something the "Filing Copy" that makes something part of the transmission file, as the "Filing Copy" has allows the preparer to make choices on what to include in that copy just like the "Client Copy" and "Preparer Copy".