If a ship is wearing the tag assigned to your official faction, it is considered a part of that official faction.
If a ships is part of an official faction, it must comply with the requirements listed on the primary ID, or be within the regulations established by the faction writeup as approved at time of officialdom for those certain special cases.
The only time a secondary ID can be used is when it is approved by the administration, and the only IDs that are eligible for use as secondary are generic IDs. Freelancer, Mercenary, et cetera.
The administration hasn't approved special cases for Kruger. No secondary ID has been approved, and will not be approved for a RM ID. Which means all ships associated wearing a Kruger tag and associated with the Kruger faction should be wearing a Kruger ID. The current Kruger ID doesn't allow for Gunboats.
The simplest solution is to just untag the gunboats, guys, and run them as RM indies.
