Gotta disagree with you on native language dictionaries. Even in my best language, Spanish, where I am conversationally fluent, dictionary definitions are often impenetrable.
For instance: I could make a card with sapo on one side and the dictionary definition anfibio anuro de cuerpo rechoncho y robusto, ojos saltones, extremidades cortas y piel de aspecto verrugoso on the other.
But words I don't know in this definition are: anuro, rechoncho, I'm not sure what robusto means here, or verrugoso.
The definition of anuro is: Que carece de cola.
I don't know carecer.
Carecer means lacking. Ok. So anuro means lacking a tail.
Rechoncho defines as grueso y de poca altura ok--so thick and short.
verrugoso means que tiene verrugas ok and verruga means excrecencia cutánea por lo general redonda.
Exrecencia means Protuberancia, generalmente carnosa, que se produce en animales y plantas, alterando su textura y superficie natural.
but....
**Or **
I could just write frog.
I'm guessing you're a reader, but my interest in languages is mainly in conversation, which has a significantly smaller vocabulary; I make do with word reference bilingual.
I agree with you on everything else. The true nuance of a word is learned, as you say, from context, so knowing the root/literal meaning of a word is the core of what your anki study can give you. I used to learn all the different definitions, but usually there is a core meaning and the other meanings are merely metaphorical extensions, and it's good to practice staying flexible.