Well, seems like you are going to have a washer and nut set up no matter what you do. Can't see how having that on both ends would make it that much weaker.I would never secure the engine in my bike with threaded rod. Respectfully I think it is just too weak and my experience through out my life has shown that to be true many times. A threaded rod does not even have the strenth of a grade 2 or Class 8.8 metric bolt. I Googled "is thread rod as strong as a grade 2 bolt and got this.
Because the minor diameter (valley) of the threads is significantly less than the full size diameter of the shank on a headed bolt, the rod with nut often breaks at a much lower strength than a headed bolt. More importantly, even if the rod with nut does develop enough strength to meet the specification, it will often break at the junction of the nut which is acting as the head of the bolt when wedge tested per ASTM F606. For this reason, technically a rod with nut in lieu of a headed bolt will frequently fail mechanical testing because the head (nut in this case) comes off before the bolt breaks in the body or threaded section of the fastener which constitutes an automatic failure.
If it was holding on my muffler maybe but would it hold my engine? What about a crash? FWIW just my opinion.