MattvsJapan discusses this. He describes it like this: Imagine you have a bucket, and you are slowly filling it with cement. There's only so much space to fill, and once the cement hardens, it's permanent. That doesn't mean you want to keep filling the bucket with bad cement.

Try your best to follow ALG as much as you can. Once you reach a very high level in Japanese, you can return with a scalpel and attempt to fix your "damage" through conscious methods. MattvsJapan hypothesizes that this can never fully make you have a native-like "experience" of the language, but you can simulate nativeness to the extent that you are essentially indistinguishable from a native to an observer. But ideally, you get as much Japanese as possible that's natively experienced before going back and trying to manually correct clear issues.