Radial Attachment Point can't have the top node closer to the root part
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When two vessels are docked via a regular construction port, the two ports won't compress if there is a radial attachment point in the vessel tree, and the attachment point's top node is closer to the root part. If the root part of the vessel tree is connected to the attachment point via the bottom node, then the construction ports compress fine.
See the attached save game file. I constructed a rover with all stock parts, except for the construction ports. Rover A is further from the runway. Rover B is closer to the runway. Rover A is a probe, while Rover B is a station. When you dock them, Rover B becomes the root part, and you can compress construction ports. This is because the radial attachment port on B (on the end with all the communotrons) is attached to the fuel tank via the attachment point's bottom node, and the tank is attached to the root part.
Now change Rover A to be a station, and Rover B to be a probe, and dock them. Rover B is now the root part. When you attempt to compress the ports, you get an error on the console ("It is illegal for a joint to connect a rigid body to itself."), and the attachment point doesn't connect to the adapter. This is because the attachment point would have its top node connected to the adapter, which connects to the fuel tank, which in turn connects to the root part.
The difference is that when the root part is connected to the attachment point via the top node, it breaks. If the root part is connected to the attachment point via the bottom node, everything is fine.
Possibly related to this issue: https://www.youtube.com/watch?v=fe06rhjjeY8&feature=youtu.be.
Basically it looks likes construction ignores the "BZ-52 Radial Attachment Point" and wants to connect to the modded copula module instead, but KSP is like nope.