Even with the use of the Black Boxes, Hanse knew his nation couldn't function effectively while under interdiction. That's one of the primary reasons his war ended.
Hanse is not the first ruler to oppose ComStar. (Look for various "secret wars" in House sourcebooks, handbooks, or the ComStar SB.)
ComStar may run the port authority, locally, on various inconsequential worlds. But what need is there for a sphere-wide bureaucracy tracking ships? Any arbitration ComStar might be called on to do in that regard would surely be handled as part of their normal banking duties, or through the MRBC, rather than creating a whole separate bureaucratic arm.
And to reiterate: I don't see what effect you think this has on the point I was making.