The rubber cushion is a good idea. Your choice of mounting does depend on precision of hole drilling. The standard "kit" solution is larger holes to accommodate. That does lead to shifting due to vibration in the long term. I understand the manufacturing point but have resorted to larger bolts to reduce play in the standard hole.

My experience in a similar situation was that I won a rack in a raffle. The rack was wider than my Jeep Cherokee would accommodate.

My solution was to trim about 6 inches in rack width to accommodate the ConFer rack mounting hardware that I had excess of.

So, with roof racks, achieving a tight clamp on the gutter is important. There is no perfect fit and providing the rubber cushion will go a long way to attaining a positive clamp. That is critical.

Good job on your design and build. Thanks for sharing and addressing my critique...