The connection on a bell housing bolt should be a pathway directly to the engine block, with some degradation over time. That should not be going through the front pump unless the connection degrades. But it becomes another parallel circuit, now flowing some current. How much current depends on the main block to battery to frame connection at the passenger lower front of the engine block. When that connection degrades, current flow increases through the other pathways. When it gets poor enough, you usually find the 12ga braided cable under the footwell burn up, occurring when the starter is engaged. The starter is a hungry beast for a short time and will alter the flow throughout the braided cables. Early Powerstrokes had a recall to improve the primary connection, changing the stud and the tension. It also warned about the block to firewall 12ga braided cable being burned, but it never mentioned the footwell cable, which is the one that has a higher occurrence of burnout.
I'm not a fan of the OE layout and have made several videos about the negative pathways. I've also had videos of improving battery to battery and the need to add another 8ga negative cable from the driver's battery to the driver's side inner fender. The battery to battery was showing a method to help, although it's still not ideal. It was not to have people pay a ridiculous amount of money for a popular set. I still have two more videos to finish the group; why the 8ga negative is needed and a better design main cable set, well, maybe two different ways.
Back to the question, adding a cable to the trans, which Ford says not to do, adds a potential pathway that could do damage if the starter current goes through the trans. So it's better to make sure the primary connection is good every few years.
The existing cables as they exist are very dynamic, altering flow direction between key-on, starter engagement, and running. This work was done before the ideal of a trans cable was brought up or I would have added that to the tests. I still might at some point, but I've got enough on my plate.