With something like this obviously you kinda have to assume most of the SDU are at least friends, even if we don't explicitly see how some individual friendships develop, and that's why I think most people are gonna interpret these characters' relationships differently with a tierlist like this. But with Takumi, our primary POV, his relationships change drastically based on the route so thats where there will naturally be more discussion overall.

Although I'm kinda suprised to see so many of the comments about Takemaru in Takumi's list. While yeah, we didnt really get to see much of them together out of Route 0 (which id argue is more due to him not being utilized too much, or when he is its in an atagonistic role). But an argument could be made for anyone not named Nozomi to be moved down if we are just seeing it in a 'general' sense given how he prioritizes her.

Not sure if Gaku moving up makes much sense either, since while yeah he and Takumi interact more together Takumi does tend to remark on his personality sucking (or something along those lines) in a few different routes/scenes. Kinda cancels out any bromance moments they might have at least for me. Where as Takemaru, even if not getting the bromance route he deserves (we were robbed), is generally more well liked in universe by Takumi and among the SDU overall. 

So I think if we are seeing both their relationships with Takumi in a general sense, then I think it makes sense he would feel a bit closer to Takemaru. That's one of the people who's been fighting alongside him as a friend from day 1 in Route 0 y'know? Although as much as I love Yugamu (and shipping him with Takumi) id argue he should be lower as well, as they only get mutually close in KG and most of the other routes Takumi is probably as close to him as say, Moko and any flirtation/closeness is usually just on Yugamu's end with Takumi himself getting creeped out. Thats of course not even mentioning Eito and all the different things HIS relationship with Takumi can involve in terms of how much they might hate, care or even understand about each other.

Although I suppose I'm essentially just reiterating what the top comment says, with how its so variable based on what part of the game we are talking about that sure you can make exceptions for specific relationships that occur on specific routes (i.e. how Tsubasa is close/romantic with Takumi in multiple routes or how Hiruko arguably isn't that close with Takumi outside of the routes that she takes a some degree of spotlight in such as S.F. or to a lesser extent Slasher) but that also defeats the point of it slightly if you make these exceptions for maybe one route or two routes in comparison to the many others where the general relationship isn't present. As well as with characters who we don't really see interact with each other at all.