Hey there, I’m a beginner student (N5, studying for N4) and I have been using Wanikani and Bunpro for learning vocabulary, but while Bunpro’s sentence examples may be useful, I’m starting to feel that Japanese has an higher level of abstraction that I’m finding difficult to grasp. I refer to those words (usually verbs) that seem to have a lot of different meanings, like “掛かる” (かこる).
Do you have any suggestions to study words more as concepts, in a more abstract way, instead of relating them simply to their translation?
Would other platforms like Satori reader or Human Japanese be helpful in this regard?
To be honest, if you are going to learn all the meaning of those very common word such as かける/ かかる、あげる/あがる、とる。。。, its gonna take too long. So for those word, I suggest learning those top 2 or 3 meanings. And keep leaning other meanings through example later down the line. Those specific words really need comtext to be clearly defined.
Piggybacking off of what Minh_Nguyen said, I think this type of stuff is best learned naturally via immersion rather than actively studying it. A lot of times, these types of verbs will have a general sense of what they mean, and this manifests in different ways depending on the context. I can’t think of a great example off the top of my head (and I’m probably not qualified to give one anyhow), but I have seen quite a few explanations on Satori reader that talk about words like this, so I do think Satori reader would be a good platform for exposure to this type of stuff. I also think it’s a really good learning platform in general, and you can read quite a bit of stuff for free to get a sense of what the platform is like. You can also get a discount with this link Satori Reader | New Subscription from the video that Tokini Andy did on Satori Reader. (I’m not sponsored, just really like the website lol.)
I would not say that Japanese has a higher level of abstraction in this regard. The words you’re thinking about (かかる is a great example) are the kind of word you likely don’t even notice in English.
Take ‘Run’. This word has over 640 listed definitions in the OED. You can run across the street. You can run an app on your phone. You can run for office. Your nose can run. A play can run for just a mere two weeks. Your blonde hair can run in the family. You can run a red light. You can run a car off the road. You can run contraband into the country. You can run a risk. You can run the tables with a run of cards to afford a big run of grassland for you and your family to run.
So, seriously, don’t worry about this. You will get the hang of it.
It is best to learn collocation pairs instead of just the word in isolation. For example:
電話がかかる
食事をする vs ご飯を食べる
I will always suggest reading as a great way to build vocab and see it used naturally.
We have these in English too.
“Why does get have so many meanings?” Is a question Japanese people have asked me 3 times.
I think in abstraction
掛かる is on. ‘sit down’ - well you are sitting on a chair so OK. Answer the phone - well. The phone is on, so sure
Come up with an example like that for each meaning.
Seeing them all listed out like bunpro does is overwhelming, but if you read the example sentences, and take it slow it’s totally doable
Good luck 
I’ve always conceptualized かける/かかる as a “hanging” of some sort.
腰かける・to sit (park your butt/hang up your butt/waist on a seat)
見かける・to notice (imagine you’re scanning around, but your vision/gaze gets caught up on something)
電話をかける・to call (landline phone receiver wedged into your neck/shoulder)
心配をかける・to make worry (like sticking bad juju/voodoo on someone - hanging worry off them)
kinda similar to how に付き gets used sometimes
通りかかる・to happen to pass by (like you’re walking down a street and a cartoon vaudeville hook stops you - you got caught up/hung up while out)
A little mental gymnastics goes a long way. I wont profess this to be foolproof or whatever though.
With respect to your broader question though, I find that (in addition to the aforementioned mental gymnastics) simply seeing how it used helps. Trying to get a large and diverse swathe of examples - and mass ingestion of said examples - helps narrow in on the ‘feel’ of a word. Especially helpful if your source has English translations and you can compare your own mental translation to the one provided. In practical terms this is just finding a bunch of examples that don’t all follow the same exact pattern, e.g. if we’re talking about 「心配」, 1000 examples of 「心配しないで」 isn’t super helpful.
I’m not sure about abstraction, but Japanese does have a lot of idiomatic words (but then so does English), and sure lots of words have multiple meanings but that’s true in many (all?) languages. However the Japanese do have a habit of talking around a topic. Often as a result the actual point of what’s being said is left to implication, which I certainly feel leads to abstract sentences.
As other’s have said its mostly something you get used to with practice, reading is good because you don’t have a time limit to comprehend. I wouldn’t recommend changing platform just consuming a lot of whatever media interests you (and you can cope with at your level).
Good luck, any approach persisted with will eventually yield results.