Do On and Kun readings actually make sense or follow any logic?

Okay so i've recently started to learn kanji and have found a big point with which i'm struggling.
For some kanji (most kanji it seems), On and Kun readings seem to mean the same thing, but aren’t interchangeable
I am using the Chase Colburn kanji app (recommended to me on this very sub) which is wonderful, and it has some reading exercises
The first of these is 1日がごとに. While the app tells me what this means and the reading it uses, i looked up the sentence and apparently, depending on the reading of 一 and日 it can both mean "every day" and "once per day" which don’t mean the same thing, could be hard to distinguish from context and could lead to mistakes
Similarly, 木 means tree with both readings, but apparently thzy aren’t interchangeable? How do you know?

Is there a logic behind which reading is used for what purpose or do you just have to guess/know all of them? Also what about cases (like my sentence) where context can’t be used to tell them apart but both are contradictory or vastly different in meaning?

Also about these easy reading exercises, they are centered about 1 kanji per sentence (in the beginning stages, with a kanji i know) but i don’t know what the rest of the sentences mean. Does anyone have a good vocab learning method? I feel like it would be useful to learn both in parallel, as well as grammar/particles

Thanks in advance!

by Emotional-Brilliant9

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