Seed coat color depends on the accumulation of plant pigments like cyanidin 3-00-D-glucoside and pelargonidin 3-O-0-D-glucoside in beans, catechinopyranocyanidins in small red bean (Vigna angularis), flavonoids, proanthocyanidins (condensed tannin), and some other phenolic relatives, like lignin and melanin in Brassica. Proanthocyanidins in soybean. Many of them have functions in plant resistance to pathogens. Phenolic compounds make seed coats stronger. it is a wild type of seeds. For example, soybean non-pigmented seeds do not need scarification for germination and they are easier to cook, but often the coat is damaged after the seed is matured, and it does not hold water. In soybean dark seed coat color is controlled by the mother plant, and white color - by seed siRNA:
Jia J, Ji R, Li Z, Yu Y, Nakano M, Long Y, Feng L, Qin C, Lu D, Zhan J, Xia R. Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats. The Plant Cell. 2020 Dec;32(12):3662-73.
The reality is that small seeds and pigmented seeds can associate with greater ability to maintain seed viability in storage and promote growth under difficult field conditions.
Also these compounds are also astringent and can limit some food and feed usages.
Small, pigmented seeds can require scarification as our colleague suggested.
Dark pigments can serve as anit oxidants which oxidization being a critical aging process.
Pigments are also agents of antifeeding inhibition of weed seed and pathogens.
The melanin pigment is found in plants animals and microbes and is well known to be a UV protector.
Recently in Chernobyl the damaged reactors were found covered in black yeast browth and the ability of the melanogic yeasts is to transform the ionizing radiation into beneficial heat used by yeast to favor its survival and prolieration.
Dark pigments have apparently advantages for environmental tlerance and energetic transformations.
Albino mutants of various types have very severe mutiple issues. While darker is not always better there is so ability for pigments to serve very needed roles and possess interesting capacities.