Is there always only one “correct” way of breaking a kanji down into components and is the way that WaniKani shows always the correct one?
For example, WaniKani breaks down 直 as lion + cross + eye. Is there any reason to prefer this breakdown vs. lion + ground + self.
In such cases I usually note all the ways to breakdown the kanji and use which ever I find the easiest:
No. Also, WaniKani breaks things down based on the mnemonics they create. The way they do it is basically completely subjective.
And to note, many of its radicals are not always the same radicals you would find in use in either Japanese or Chinese character dictionaries.
No, it’s just the way they decided to break it down to create the mnemonic device. You can create your own mnemonic using the breakdown of radicals that you prefer if you want. I would note, though, that your breakdown fails to account for the horizontal stroke at the type of the kanji. This is why most dictionaries will likely break it down as the ‘eye’ and ‘ten’ radicals.
Just as an example, if you were to look up this kanji on JapanDict the radical break down they use is:
This is because ‘Lion’ is one of those WK ‘fake’ radicals.
Edit to add:
I’m now wondering if you aren’t viewing this kanji using a Chinese font rather than Japanese which will change the way the font is rendered in a browser.
You may be seeing it rendered as the middle version rather than the top version which may be the source of your confusion. 
In fact, the symbol that appears on the radical card is quite literally the English letter L. 
In the lion + ground + self breakdown I was thinking, ground was supposed to be referring to the horizontal stroke at the top of the kanji (see blow). Are you saying there is some reason why dictionaries typically would not do that?
Stroke order of writing the kanji most likely. It’s written exactly as you would when it’s a combo of 十 and 目.
Isn’t the stroke order for a combo of 十 and 目 the same as the stroke order for a combo of ground (at the top) and 自?
They do for some kanji that doesn’t have the “cross” part at the top 
This is the kanji for summer: 夏
You can see they have listed the parts for “ground”, “winter”, “eye” and “self”.
(source: https://jisho.org/search/夏%20%23kanji)
Do you know if there a reason they don’t include leaf or vertical line for the kanji you mentioned?
There is always some true historical composition, but it’s not necessarily critical for you to use that when making a mnemonic. (and due to historical simplifications or changes, the true historical composition may not even be readily apparent without research)
Will “official” resources like Japanese dictionaries generally be consistent or is there a fair amount of variation? I notice that Jisho and JapanDict both give the exact same breakdown of 直.
That’s because Jisho and KanjiDict both use the same kanji database for their information. You can see it on the about / attributions pages. Also, that info is just there for convenience’s sake in doing manual radical searches, it’s not meant to be authoritative.
It’s possible for there to be disagreement over some things, like what the purpose of a given element was. Like one dictionary might say it was only phonetic, and another might say that it also contributed a meaning to the kanji as well, but they typically won’t disagree on what was actually there. I would recommend actual monolingual kanji dictionaries that include a 成り立ち explanation though.
There are a lot of folk etymologies and things online, basically the same idea as our mnemonics.
What’s with all your little windows? Are you using some programme?
Yes, the one I wrote myself for taking notes.
I like sticky note apps, so I was curious if I could make one myself - turned out, I can, though I’m probably the only one who’d find it comfortable to use 
If you want a similar but more comfortable experience, I recommend MS OneNote.
If you look closely the kanji uses 十 and 目 and not a combination of 一 自.
At the very top there is a head sticking out and is not flat on top. 直 compared to like 百 which is more similar to what you are refering to.
Now while the parts of these kanji are different I think they make my point about the little head on the top of 直. To my knowledge, at least in the 5 mins of looking at jisho.org, there isn’t a kanji like this diagram.
EDIT: Also how Redglare also refered to 夏 not having the top bit is a better reference than 百 but I’m going to leave this as is.
If I understand correctly, are you saying that while it is common for different components of a kanji to touch, it is uncommon for different components of a kanji to have strokes that completely cross through each other? Since the top horizontal and top downward strokes in 直 completely cross through each other, one would surmise they aren’t part of different components?
Essentially, yes, but also there’s the fact that a dot - like the top stroke of 自 - is quite different in essence to a vertical line - like the top stroke of 直.
Along with what Belthazar said, you also can’t really trust the font sometimes.
市 is an example that for the longest time I thought was only 4 strokes when it is actually 5. The line the looks like it run through the middle of the character is actually 2 different strokes. One dot on the top and another line from the 一 down.
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