What exactly are the limitations with regards to referencing real-world copyrighted pop culture in media?

I’ve been reading ドメスティックな彼女 (Domestic Girlfriend) recently, and I’ve noticed That it sometimes makes direct references to real life pop culture. Sometimes, they don’t bother to censor, hide, or otherwise just make a slight modification to names.

For example, in the first volume, Rui gives examples of old songs she likes, and you can track them down on YouTube no problem since the author outright tells you the title without any effort to hide it. In another volume, Al actually sings a song. The lyrics were right there in speech bubbles.

The characters also consistently use LINE, and I think a background character might have also mentioned Twitter. Another thing was The Simpsons. Natsuo had the logo on his shirt. I don’t just mean text that says “the” and “simpsons” in close proximity to each other either. I mean that it has the letters just as the actual logo has it. “T” with the lines crossing, capital “H”, lowercase “e”, a considerably big “S”, etc. In the anime, this detail was replaced with a tourist shirt.

And yet, they’ll censor stuff like Calpis and UNIQLO rendering it like “カル◯ス” and “ユニ○ロ” when characters say these brands aloud. And one of the contexts for these was “ユニ○ロ万歳だな…” when >!Natsuo and Rui go on a trip in the snow without wearing warm enough clothing!<, so it’s not like they’re saying bad things about the brand.

So what’s the deal? Most anime I’ve seen censor stuff like LINE, calling it “LIME” or something instead. Why not here? I suppose the author would have had to get some legal permissions to mention some of these things, but I’m curious as to what the rules are, and what is and isn’t allowed.