I absolutely adore the richness you put into everything you make. However, whilst I understand the appeal of the "small-but-smart" character, and there certainly are a lot of very smart tiny people, I don't quite understand why one would think being tiny would make them smarter given that IQ is mostly heritable, even more so in impoverished, low-resource environments, and increased height is actually slightly correlated with increased IQ. I acknowledge that IQ is somewhat plastic to the environment early in development, and admittedly his is more the case where this guy comes from, as poverty decreases the heritability of IQ. However, the environmental variable you speak of probably wouldn't affect it positively.
Something more plausible would be that this runty guy's smarts represent random variation within the population, or, tangent time; if you want to go with something fun perhaps his developmental plasticity was drastically enhanced throughout his childhood and adolescence, as unlike the rest he would spend time finding and eating the local small yellow berries. Their pigment was the yellow flavonoid 7,8-dihydroxyflavone, an orally bioavailable TrkB agonist which partially mimics BDNF(Brain Derived Neurotrophic Factor), enhancing memory, neurogenesesis, synaptogenesis and brain growth in general. Admittedly, someone would have to be very smart and not a throwaway character for you to bother with this kind of backstory.