Good question -- for which I have no definitive answer aside from saying that choṭā is fine sounding for "younger* in this case, and I think it would be the default understanding. If you need to specify size, छोटे कद का should work, and if specifying age, I believe छोटी उमर का will do it!
Colloquially we say, "He is my little brother." for "He is my younger brother." Children sometimes say, "He is littler than me." for "He is younger than me." but never "He is smaller/shorter than me" to refer to age. The context usually makes if clear that age rather than size is meant for '"little, littler", but it does seem that the Hindi usage is more ambiguous as to size or age. Do you Hindi speakers ever find छोटा ambiguous?