Duplicate Parking
Not a problem, if they don't use a jetway. All those duplicate parking don't have jetways.
Altitude
1mm difference ? FSX can't even resolve that, because the smallest altitude difference in the AFCAD is 1/128th of a meter.
Open links
There aren't any. They are mistakenly reported as such because they are vehicles paths intentionally made in order not to cross normal apron links.
Jetway use.
Not a problem either. They are reported as errors by ADE, because the parking is intentionally flagged as GA to get rid of default ground vehicles (like all our airports), but they have a jetway, and ADE finds this to be strange, but it's not really an issue, the jetway works.
Is there any chance of getting a new Afcad which resolves the problem.
There are other things that can be improved, like adjusting some parking size and adding some GA parkings, but none of these are problems.