Immune System Recognized Implants
During the development of a fetus, there is a window where the nascent immune system takes note of all of the surface enzymes on all of the cells in the fetus. It "remembers" these and considers them "self" cells. From that point through the rest of the life of the organism, the immune system will attack all non-"self" cells.
If an artificial surface enzyme can be created that is composed of amino acids unused by Earth-based life, but for which receptors can be made from life's standard array of amino acids, these can be used 100% safely on artificially implanted matter. The immune system of the fetus would identify them as "self" during that window, however, as the receptor cannot be made with the amino acids available to naturally occurring life, it would be impossible for a pathogen to duplicate them. Thus adding this surface enzyme to the fetus's normal array would incur no additional threat to the health of the organism.
After the fetus develops and is born, the organism's body can be implanted with anything imaginable, as long as the proposed implant can be coated with these surface enzymes. The immune system will ignore the implant and will attack as usual any other foreign life or matter introduced during the implantation process. Potentially, the patient's immune system could be cultivated ex-vitro, and the implant could be pretreated with this cultivation, "cleaning" it before implantation.
This opens the door to all kinds of fully integratable implants to solve all kinds of problems that were previously intractable due to immune system rejection.