I made a custom mini-base 3x5x5 blocks with just a small gen/console/ fuel tank, with the "repair block" on the side a few blocks distance from the "base". When I need repairs I spawn the base and then I simply drive the "nose" of my CV to touch the block and it works fine. Now that I see it "out of the game" I'm thinking of a different design...
I think it's "normal" since the game has to decide what to repair, and can't sort it if there are 2 builds intersecting with the bounding box. We just have to keep this in mind when building "repair areas" but I usually go in space - much simpler there.
My repair facilities come in two varieties: 1. The large, flat pad. Exactly what it sounds like, a very large, very flat pad, with a repair bay block. I've built these in sizes up to 75x50 to accommodate my larger CV's. They're not very exciting, but they work just fine. 2. The Upside-Down Space Dock. This is a weird one, and requires some very peculiar building - it's a variation on the Large Flat Pad, except that the facility is build upside down, so that the repair bay is at the "top" of the structure. Ships fly in and park under it to make repairs. Either of these designs work quite well, and have not produced a "there's something in the way" error. A third variation I've used on planets is the the MicroCV, which is a CV with a repair bay, generator and fuel tank. Once it's placed, it remains immobile, but does allow a little skirting of the One-Repair-Bay-Per-Base rule. This is great for maintaining SV's and HV's As for the OP - as has been stated, the Repair Blocks mode will repair damage to all blocks. Repair to Template replaces missing blocks, so long as you: a. Saved a Template b. Have not added anything that has since gone missing since the last time you a. Saved a Template. If you find blocks are not being repaired in the Repair Blocks mode, file a bug report, as bugs do happen.
