He might be thinking like what Lurker did in RSRDC in SH4, in that he made a few ships as copies, but set to be "Environmental" objects, and set them to be invisible so that they could be used as "targets" for the SpecOps Photo Recon missions, but in this case, you'd use them as visible, "stationary" docked ships. ?? - maybe...
This does sound a bit like SH4 with docked ships, where the sea movement will cause the ship to drift, and if you're setting them yourself, you have to "merge" the layers (without Save, of course), so that you can "see" where you are placing things, compared to each layer. If a particular file runs throughout the game with multiple spawns to occur into the same dock "space", then you run into issues when the game detects a ship has "moved" and spawns another in the original's space, even though in actuality, it's only drifted a few feet. Then they "bump" each other around and try to avoid "collisions" with each other, and you can have all sorts of mayhem occurring, including ships "merged" into docks and other shore side emplacements - not forgetting the fire and destruction of some of the "collisions"... Stock SH3 and SH4 are very similar in this regard. I wouldn't be surprised to find that SH5 is done the same way in stock trim. The HarborTraffic files are the worst in SH4, but the NavalBases aren't too far behind...