The direct answer to your question is that the meaning of 'understand' is not a composition of its parts, as you have well noticed, and this is a general feature of natural languages that it is not logical or literal. It might start off literally (as in a constructed language) but once a generation has gone by, everything is metaphorical. For example there are similar words 'undertake', 'forget', 'withold''withhold' whose meanings are only tangentially related to their parts.
As to the particular phenomenon of 'understand', etymonline has a speculative derivation where 'under' really comes from the PIE root for 'inter' or between (thus, thus an attempt at preserving some literal connection in the ancient word.
For comparison as to how other languages do it for 'understand', there is quite a bit of 'illogical'illogical non-literal metaphor: 'com-prendre' in French and Spanish (literally 'take with'), 'по-нимать' (Russian - 'takes on'), 'κατα-λαβαίνω'λαμβάνω' (Greek 'get at'hold down'). Ofc ourseOf course all these examples are European, so there may be aan area influence (Sprachbund). I was unable to confirm examples in Indian or Chinese (most terms in Chinese really are pairs of syllables each with tehirtheir own stand alone meaning) so often a metaphorical extension occurs anyway).