The only words I’ve SRS’d which contain WK kanji that I haven’t learned yet are some of my textbook vocabulary. It wasn’t really a problem for me in that case because Minna no Nihongo has furigana, so I just learned the words by their readings and didn’t even attempt to memorize the kanji, though sometimes I did by accident. If the words are in WK, I’ll often look them up in advance and take advantage of the mnemonic.
I didn’t start actively mining my own words from native media until I was over 20 levels in. By the mid 20’s, I had such a strong base of kanji knowledge from WK, I had no shortage of new words I could add to Anki from my reading which contained only kanji that I had already learned. So I’ve simply never even bothered to learn WK kanji early. I’ll just use a dictionary/Yomichan to look up the meaning of words with unknown kanji, and then move on.
Some people try to prioritize their vocab/kanji acquisition by aiming for the most common words/kanji first, but for the media I’m most interested in, this is pretty much impossible to determine anyway, so I’m just prioritizing learning words that contain kanji I currently know (which is a constantly growing number). This is keeping me plenty busy, and it’s actually kind of nice because it takes a lot of decisions out of my hands. Theoretically, by the time I do reach level 60, I’ll have built up enough of a base of vocab from the lower level stuff, I can just add everything I don’t know to Anki.
I have also started learning kanji that aren’t in WK’s system, though I’m pretty lax on this currently. I don’t check every unknown kanji I come across to see if it’s in WK or not, but if I do notice that one isn’t, usually I’ll make a card for it in Anki. So far, I’ve learned about 12 non-WK kanji. Once I’m level 60, I’ll start adding all new kanji that I come across to Anki.
There are many strategies for learning kanji on your own. Mine is probably unpopular, because it involves testing me on how well I can write them from memory, haha. I use the Kanji colorizer Anki addon to create recall cards, and then also have recognition cards which ask me for the same types of info that WK does (reading and meaning, though I’m more lenient on grading myself with meaning outside of WK, because for many kanji, especially those in names, it’s just not really relevant). So far, this strategy has worked great for me, and I’ve had no trouble remembering the kanji when I see them in the wild.
I do sometimes use WK’s radicals to help me remember, but way more often than that, I use the kanji’s phonetic and semantic components. Half of the time, when I look up a kanji in WK, the information that’s most useful to me is the Keisei script info and not the default WK info.
I guess I’m not fully sure how to advise you, because in my opinion, the speed I’m currently going on WK (learning about 3 kanji a day) is plenty fast, so I see no need to want to speed things up further. WK saves me a lot of work because the flash cards are already prepared, and the Keisei script info is already set up, and I personally wouldn’t want to repeat all of that work in order to learn the kanji on my own outside of the system.
So I save my energy for kanji that aren’t in WK at all, and just wait to learn the ones that are. I’ll be done with WK in less than a year anyway, and in the meantime, it’s not like there’s a shortage of non-WK vocab and kanji that I can learn.
I definitely agree that WK and immersion can be done in tandem. In my experience, immersion has just gotten easier and easier the more kanji I’ve learned (through WK) and the more grammar and additional vocab I’ve learned. Once I reached about level 30 and graduated out of the low beginner phase of grammar, it felt like suddenly all of my accumulated knowledge came together, and immersion became much easier.
I don’t think there’s any real need to set WK aside completely unless you really don’t like it. It’s true that you can progress faster without WK, but actually implementing those strategies is a different matter. It can be kind of sink or swim. You need to be pretty self-directed and willing to sacrifice some of the ease that WK affords you, which means spending more time messing around with other tools, and more time having to put together flash cards yourself, and making more decisions about what to prioritize your time doing.