I am not well-versed in either the Drawing Management system or eTransmit, but in exploring the use of eTransmit with a Project Navigator project, I found a minor issue that I think is a bug. It could be "as designed," but I would not have designed it that way, so I will consider it a bug until enlightened otherwise. Fortunately, there is a workaround.
In Project Navigator, on the Sheet Sets tab with the Sheet Set View current, if you right-click on the Sheet Set node, the context menu includes an eTransmit Setups option.Select that option, and then either create a new setup or modify an existing setup. In the Modify Transmittal Setup dialog, in the lower-right corner, both the Include project information and the Include project default templates options are disabled. The latter should be, until the former is selected, but the former should not be disabled, in my opinion. I could find no combination of other settings in this dialog that would activate the Include project information toggle.
That same context menu, as well as the context menu that comes up when right clicking on a drawing file or folder on the Sheets, has an eTransmit option. Selecting that opens the Create Transmittal dialog, which features a Transmittal Setups button that initiates the same sequence of dialogs as the eTransmit Setups option on the context menu.When you get to the Modify Transmittal Setup dialog through this avenue, the Include project information toggle is active, and checking it activates the Include project default templates toggle, allowing you to make these settings and save them to a Transmittal Setup for later use.
Note that if you save the setup with one or both of the "project" toggles checked, and later reopen it by using the eTransmit Setups option on the Sheet Set node right-click context menu and modifying the saved setup, those options will be disabled (and no check marks will appear). That should not be a cause for alarm; in my somewhat limited testing so far, even if I made a change elsewhere in the dialog and resaved the setup, the check mark(s) were preserved when opening it through the eTransmit/Create Transmittal dialog method.
My guess is that there are times when the Include project information toggle should not be active (when accessed outside of Project Navigator, via AutoCAD Sheet Sets), that the dialog definition has it disabled by default, and enabling it when using the eTransmit Setups option got missed (or accidentally removed).