The tubes are matte black of course, and no, I haven’t noticed any flare issues. And yes, I check focus every time. This is because the rig is ‘upside down’. The camera points upwards on a tripod and the negative carrier is pressed onto a lens shade screwed into the macro lens. A lamp and diffuser are placed above the carrier. This makes the negative carrier itself easy to access – it’s on the top. The rig was made for me by a friend who has a precision laser cutter and works well, but every time you change the negative you perturb it a bit and that necessitates the refocus. It wouldn’t hurt to lubricate the lens, too, which would make focusing more precise, but focusing isn’t much of a hassle. Having autofocus would be slicker, though, for sure.
I shoot at f5.6 or f8 and, usually about 1/4 sec. I use the electronic first curtain shutter to reduce vibration.