The important question is why is your pin free? Is the pin locked into the bottom hole on the post that is designed for thicker bed liners? DO NOT tow until that condition is rectified.....
Your use of addition rubber likely won't cause a problem if it's hardness is hard enough....my preference is something harder like the UHMW B&W supplies the Chevy owners if they complain about the bed caving in.
I have not done an install on a Dodge as new as yours, but isn't there another piece of the puzzle required to make an old companion fit your application? Seems like I remember seeing an email on this subject?
I'm not that worried about the nylock nuts wearing out or the ubolts stretching. That hardware is rated plenty strong for the application. If every driver does their pre-trip, there wont be an issue. I would imagine if a person removes and installs a few times a week, it will wear out though.
I have seen many that shim between the post and the base so they don't have to loosen the ubolts...this is bad practice. All of the leverage is then on the post! I would drive it around the parking lot if needed, but would never go on the road like this.
I really like B&W's gooseneck hitches and the 5er hitch heads, but I'm now questioning the saftey of the Companion. It has occurred to me that the end user/installer is the most important link in the saftey of this hitch. I have read about and seen too many come into the shop that were installed improperly without the driver knowing any different. This is why so many products are now "Unavailable" to us now. It is impossible for the manufacturer to ensure those last few steps are done properly. Whoever has the largest bank account or insurance policy will pay regardless of who was right or wrong in the end......