It's a totally triangulated mounting position, so you are correct, it doesn't matter at all. If you were suspending both the engine and transmission from just the front engine mounts, then yes, that would put tremendous stress on the front mounts. The rubber biscuits take up any vibration and are a built in stress compensator so to speak. As I'm re-reading your post, I am realizing that you may be talking about the bolts that join the engine and tranny at the bellhousing??? There's no dangerous tension there either. Mike Knell fabricated/designed brackets for military if memory serves, so I'm pretty sure that the kit is designed well from a stress, tension point of view.
Good to see you are thinking about this stuff. That's how we all learn. The forum is a good place for information too
Davy