Kerbal Space Program

Must say wasn't immediately clear what is reported, but after some tests, believe is tied to what follows. Sorry in case I didn't catch it correctly, if so please correct me.

Before else, this issue shows somewhat differently for children parts with the ability to be surface-attached, than for parts only stack-attachable (as the docking ports). Those able to be surface-attached will join by their surface, unless a stack node is correctly oriented to match with the parent nodes or surface. But the docking ports can only be stack-attached, so will always join by one of their nodes.

Stack nodes fit with parts oriented the same direction; so in case of the docking port placed on the shorter Modular Girder Segment, it had to be first rotated 90° to stack-attach.
Radially attaching a part that was rotated, causes it to radially attach rotated. The child part changes orientation to follow the parent part surface in radial mode: but when wasn't rotated, it always presents its bottom to the parent surface; when rotated, it presents one of its sides (or rather, causes the attachment by its stack nodes to remain rotated).
Screesnhot233 shows what I'm getting from radially attaching the two docking ports. The top port (now radially attached to the XL girder segment) is attached by its bottom as would be expected; the side port (radially attached to the shorter girder segment) presents the side.
Also to be noted that the docking port gets half-buried in the parent part, because doesn't have other than the stack node to connect. If the port had the ability to get attached by its surface (like e.g. FL-T100 fuel tank) it would still get rotated but the connection would happen on its surface instead, not involving its stack node.

Is to be noted that the issue isn't new. Tested with KSP 1.4.5 (build 2243), 1.2.2.(1622) and 0.90(705) and got exactly the same in all versions (screenshot3 from build 705). Can't say if it will be considered a real bug or "behaviour according to design", after all these years is even hard to tell what the original design was but in any case this needs be evaluated again. Certainly time it was reported in case of a bug.