The usual recommendations for touch-up paint - unless the manufacturer can provide - is nail varnish - probably not so good for a matte bike - (scale) model builder's enamel - will have matte - or car touch-up paint - probably not available as matte either.
For protection for glossy paints you can get wear-resistant transparent tape patches to stick on. These are usually meant to go on where there is cable rub, so may be too small for your liking.
For retouch, my money is on model builder's enamel. For protection, wrapping exposed parts in an old inner tube is a time-tested trick.