I started Wanikani at N3 level, took a 2 year break, then came back after getting to N1, and now there are a fair amount of words I’m familiar with but don’t know the kanji for. Those ones are a lot easier, for sure, my worry was that in a context sentence I would be able to recognize one of those words in a sentence without actually reading the kanji, which felt like cheating.
After using the script it doesn’t feel gratuitous at all though. Reading the context sentence has given me the answer several times I probably would have gotten it wrong otherwise, but that’s pretty rare, and like you said it feels legitimate because it’s a realistic way of figuring out the word, as in reading. And it’s not like the kanji becomes invisible when you figure it out from context anyway.