I think the most important thing is checking in with yourself. Considering how you’ve been going through grammar, I see no reason you shouldn’t be able to do fully comprehensive reading without a problem (if you so wish).
Also, varying your approach even with the same work is absolutely fine. Maybe one of the stories in the graded reader is so uninteresting to you, that the best thing to do if you still want to read it, is to just read it without lookups. And for another story, you might want to fully understand it and therefore look up everything until you have a full (or close to full) comprehension.
Even in learning, I personally look for enjoyment. That means that if there is a big difficulty spike, meaning I need to do a lot more lookups than normal, I’ll usually lower my standard of comprehension to understanding the gist, so I can move on to the next chapter/scene where the difficulty maybe isn’t as high. I’ll also usually lower my standard if I’m tired, because my patience and energy for look ups and such are much lower.
I also have some series that I read more extensively, and others I read more intensely. And in fact, I find graded readers a great place to do intensive reading. If they are only a little difficult, that is the time when digging into the few things that I don’t get gives a lot of results.
If you have the time and temperament for it, another approach might be to first read the (graded reader) story once without look ups, just to see how much you understand and then on a second read dig into all the areas of confusion/low comprehension. (I personally don’t have the temperament for that 95% of the time, so it isn’t an approach I use, but I’ve seen many talk about using it here on the forum.)
Ultimately there is no one strategy that is best, nor even one strategy that will always be best for you.
And with the Takagi manga, you have the aid of the book club, meaning both vocabulary sheet and grammar questions from other people already answered. So you could either go for full comprehension and use both what is there and ask additional questions when you don’t get it, or use the provided resources to do a more extensive method by using the vocab sheet and in the existing discussion threads to read as quickly/extensively as possible (without additional research for yourself).
I would say either option is useful. It all depends on what you find the most useful and/or most enjoyable.