The other reason I've heard people claim that Cyberpunk 2077 is offensive is because of the lack of relationship options for characters who don't have a "standard" combination of sex and gender traits.
From what I've heard, characters who are noticeably trans* or intersex - which is to say, characters who have any combination of sex/gender traits other than [male gender + masculine body + penis] or [female gender + feminine body + vagina] - can't romance any of the exclusively straight or exclusively gay characters. If you're playing a trans woman with a dick, the straight male and lesbian romance options aren't available to you. If you're playing a trans man with a pussy, the straight female and gay male romance options aren't available to you. There are several bisexual romance options that are available to all characters, but apparently they're all fairly minor. All of the major romantic sub-plots involve one of the four monosexual (i.e. fully straight or fully gay) characters, which means that anyone playing a noticeably trans* or intersex character will miss out on that part of the story.
Of the three complaints, this is the one that I find the most concerning. It's definitely unfortunate, and I can imagine why it would be frustrating to trans and intersex players (or anyone who just felt like playing a trans/intersex character). But is it actually transphobic? I don't know. I can't really make that call without playing/watching the game and seeing the relevant parts for myself. Is the lesbian character a TERF who goes on a long spiel about how she'll never hook up with anyone who doesn't have XX chromosomes and a vagina? I very much doubt it. Is there even a given story explanation for why she refuses to be with you if you're trans, or is the option to romance her simply not there? Was this an intentional choice by the developers at all, or just an oversight?
One of the defenses I've heard is that, due to the VERY explicit and graphic nature of the game's sex scenes, it wouldn't have been possible to simply swap out a person with boobs and a cunt for a person with a dick. Adding a trans-lesbian option (or a trans female/straight male option, or a trans male/straight female option, etc.) would've required the developers to make an entirely different set of intimate scenes, which would've required a LOT of time and effort. I'm not sure it's an entirely convincing argument (especially since it doesn't seem to have been an issue for any of the sex scenes involving bisexual women), but it's one possible explanation.
All in all, I'm in no rush to judgment here. In fact, I'm not even entirely sure that this particular claim is 100% true. And if you haven't played the game yourself, you probably shouldn't judge it on the basis of internet rumors that could easily be skewed, exaggerated, misleading, or possibly just plain false. In any event, I've already written more than enough words about a game I haven't even played yet.
*I use the term "noticeably trans" here, rather than just trans, because some trans women do have vaginas and some trans men do have penises. Sexual reassignment surgery is a thing in real life, and there's no reason to think it wouldn't exist in the setting of Cyberpunk 2077, where far more radical body modifications are possibly.