Since (in my opinion) few users use their actual name or picture in their profile, I would have assumed that active discrimination should be less of an issue here. If my assumption is correct, why do these groups still feel unwelcome?
If it is not active discrimination, are there identifiable other reasons?
Yes, a lot of users do use their actual name, whether it's the first name or a part of their own name, or their own profile picture. Though a large amount of users still use usernames. Whether a username is used or not, it may, or may not lead to more discrimination.
Though, to be honest, I don't think gender and ethnicity drives much action here on Stack Overflow. That'S (O|E) can be considered hostile to newcomers, that honestly wouldn't surprise me. There are a lot of people who post without reading the FAQ's the tour, etc., and misunderstand how the site works. I.e. posting comments as answers is something that, on Stack Overflow, happens possibly hundreds of times per day, and most of these posts (saying posts because they're posted as answers, while they're comments, or votes depending on the type) get downvoted. Duplicates get downvoted, (on Stack Overflow) tool requests get downvoted, TB questions get downvoted, etc.
Though I honestly don't think this is a group-related problem; this is a lack of user education. Most new users don't know what they can and can't post on Stack Overflow. Though the topic of user education and that is a separate topic for another time.
Anyways, as far as I can see, the Stack Exchange network moderates by content. There are, as with everywhere else, exceptions, but that's my general opinion of it. From what I've seen in general related to reviews and downvotes, gender, ethnicity, religion, etc. doesn't matter1.
Though, it's worth mentioning the blog post:
Too many people experience Stack Overflow¹ as a hostile or elitist place, especially newer coders, women, people of color, and others in marginalized groups.
As I already mentioned, new coders doesn't surprise me. As for women, people of color, and other marginalized groups, is there really any data to back that up? I've never experienced any of it (I might of course have been "lucky" or whatever it's appropriate to call it), but in the end it boils down to the quality of the post, not the poster. And I'm not saying "discrimination never happens on the basis of the poster being in a marginalized group", but downvotes are rarely cast because of the poster being who they are. In my opinion, the hostility some people experience isn't because they're a part of a marginalized group, but more because of post quality. A good post gets upvotes and generally positive responses, independently of who posted it.
Racism and sexism is, in my opinion, not a big problem. I'm not saying it never happens, but it's far from common that a post gets downvoted because the OP is, e.g. a woman. In my opinion, it looks like a majority of new users in the Stack Exchange network think downvotes are personal (that downvotes symbolize "you're wrong", "you suck", etc.). See this related MSO discussion. The problem also created a feature request for hiding scores under 0 for low-rep users.
TL;DR For most users, with extremely few exceptions it's the content of the post that gets judged, not the OP's gender, ethnicity, religion etc.
Although I do agree Stack Overflow (and the rest of the Stack Exchange network) has some problems with the handling of new users, these problems are usually caused by the post. If the OP posts a low-quality post regardless of rep, how the community responds is usually the same (downvotes, closevotes or delete votes (depending on which applies), and few comments).
There are cases where there are people who actually try helping the poster improve their post (where such applies; there isn't as much to fix on clear duplicates, but if there's missing code there's a possibility that other people try helping OP creating a good post. And the reason I again mention post quality is because I believe this is where Stack Overflow could improve. If new users are "trained" better, they might learn how to post better. Better post quality would mean fewer downvotes, getting upvotes, and the OP not feeling as "badly received".
On a related note, there was a recent comment on a downvoted and now closed answer where OP thought their profile picture was the reason for the downvotes. Again using the marginalized group card. The post should be closed (No MCVE, not here to discuss that though) but the original poster took the downvotes and closing personally and thought it was on the grounds of their gender. Or at least they tried saying the person in their profile picture wasn't them.
So yes, there are people who feel their post gets judged on the grounds of them being the poster, but (in my opinion), the poster isn't actually what gets judged about a post.
As for hate in general, there are of course actual hate posts (and hate messages in chat), but these generally get deleted. They exist, but there aren't a lot of them (all though there are exception on sites that are directly targeted by hate posts. For an instance Hinduism.SE is currently seeing a heavy wave of R/A posts from the same poster).
1: With the exception of hate posts targeted at specific groups. These are, however, removed, and their existence is an exception to the network in general.