I definitely agree that it is less than ideal. However, while I'm not sure which "common word lists" you're referring to (I've seen ones that start at 10,000 words), the newspaper word lists that I've seen are at least 5 or 10 thousand words long. The entirety of the JLPT is less than 10,000 words, so I am not sure "in common word lists" or "in newspaper lists" fully equates with "N5/N4 learners will know these".
On a different metric, the Genki I and Genki II textbooks have roughly 1,200 words between the two of them. It is often said (in a general sense) that finishing Genki II will take you almost to the end of N4, so at least from the perspective of JLPT, I do not think the data is *wrong* (just not as useable as it should be).
It may be that the JLPT itself is not a great metric for grading the difficulty of the texts. However, given that many people (on renshuu and elsewhere) are following material lists that generally aim in the same direction as the JLPT, so having a different set of metrics on this one page only that (as an example) says "this is a pre-intermediate text" (level 2 out of 5, with 5 being the hardest), and they say "well, I have done the pre-intermediate word groups on renshuu, but I can't read this at all", then it's a not a great solution.
We are already in the process of expanding our renshuu jlpt lists (I've practically doubled the N5 level since we began this transition, split into Japanese Basics and Beginner Japanese), but it's still tricky. For example, いざかや is arguably not a n5 or n4 word, maybe not even n3. When you go through the N5 list itself, you realize that you can get through 500-600 "must need" words without even breaking a sweat. Adding on "common foods you may see at a grocery store or restaurant" could easily add 7-10% to it with just that one category, and then suddenly, you have (I'm just guessing here) 2,000 words for "this is the most basic level, N5".
It is still far from perfect, and I really appreciate all the feedback. In the meantime, I will try looking into the "common word" list (which is already stored in renshuu). It's kind of crazy, because the data in there often seems to defy what is "common" to us.
Example: (both N5 words)
遊ぶ
秋
秋 is in the top 500 words (group 1, where each group has 500 words), while 遊ぶ is in group 26!? (roughly rank 12,500). So going by the freq lists, a word like あそぶ (which seems pretty common to *me*) would suggest that it is not something you'd learn for quite awhile.
Of course, this is cherry picking, but there doesn't seem to be a single method that is going to give us something satisfactory.