I think that we're stumbling over a similar difference of opinion to that which comes up when we discuss Star Trek depicting 21st century issues in the 24th-or-whatever century - if you're more invested in the in-universe reality, you're likely to raise the objection that racism we would recognise from 2024 Earth being more or less the same in 2367 Moorpak IV doesn't make sense. If you're more invested in Star Trek as a vehicle for morality plays with contemporary relevance, you're more likely to find it positive that present day issues are reflected back to us from that fictional setting.
I'm quite firmly in the latter camp - the Doctor is now a black British man and to me, if we danced around the fictional universe without that having any relevance at all, we're doing a disservice to the reality in which the show is being made. And previous handwaves like 10's line to Martha did just that (despite that being one of my favourite episodes - the reality that there were black people in Shakespearean London was right there, too). RTD has matured since then. I'm just not that interested in a carefully designed documentary about what being a millennia old timelord on alien worlds would really be like, I want to watch stories that matter to us, now.
The cliché is that sci-fi is always really about the time in which it is written - to me, that's a mission statement as well an observation. The best sci-fi makes you pause and think about the time in which it is written - and this episode clearly did that. Throwing us a "phones are bad mkay" cover so we could entirely miss what was happening underneath if we were so inclined. Sci-fi doesn't always have to reach for metaphor to make its point, they did racism as actual racism. And this Doctor knew them to hate him and offered them grace anyway. Perhaps what he said is true - he's done his healing since 12.
This episode might have needed another pass on the details of the plot, I'm still unclear as to exactly why they were being eaten in alphabetical order, but the actual ideas underneath it I liked a lot and were well presented.