I used to repair the occasional Jap many years ago, and the decals came with helpful guides to ensure consistent alignment to whatever datum line was available close by - inscrutable as usual...
I've seen Commando tank and sidepanel decals placed in a variety of positions, and when I was doing commission work I simply did as the Customer requested; some giving very precise instructions.
Pre-71 Roadsters/S-Type sidepanels (with ignition lock hole) always had the decal parallel to the bottom edge, and hence the Z-Plate.
Post-71 they just seem to be pretty random - Factory Brochures are my favourite guide, and I don't think they're that consistent.