This is something I've been avoiding.
The only solution I'm currently doing is keeping the current project indoors and working on functionality/components etc.
Presumably touchups have to be a better option than a laquer over paintwork, decals and all.
I'm thinking about trying to match the colour with the appropriate pigment as this can be done with Hammerite (although not sure how this would last and I may look for an alternative), then I suppose you are stuck with a brush.
Plan B, best colour match from any auto can, with primer and lots of masking. Not nearly as noticeable as rusty patina spots?
None of this is ideal, but does go further than I've ever bothered before. And would hopefully retain the original character of the bike and look halfway decent?