Yup. And the fact that you can't even mention that you've (or at least can, depending on your playthrough) brought peace to the Geth and Quarians, thus proving the argument that "synthetics and organics cannot live in peace" is fundamentally untrue, is yet another example of why the ending of ME3 is just bad on multiple fronts.
There are literally fleets of synthetics who have joined forces with organics to fight against the Reapers as you're talking to the star child right there and then, and you can't even bring it up.
And yeah, just the whole idea of "synthesis" fundamentally flies in the face of one of the biggest themes of the series to me. You have three games where you see that despite all the differences between the various races of the galaxy, you're all stronger together, united. That diversity is a good thing. Your differences make you unique. Even Cerberus, the pro-human supremacists, have to admit that in ME2 with half the members of the team they tell you to assemble.
In every game it's a multi-species team that ends up saving the day, and in the end, the galaxy. And then synthesis comes along and makes everyone the same. It'd be like having a movie about people of different racial backgrounds struggling to get along, and then the "happy ending" is that everyone gets turned into a white guy.
The whole thing is just so busted on so many levels that one of the reasons I'm both hopeful and surprised they're actually making some sort of follow-up is that it can't help but retcon some of this mess away (I mean there's no way in hell synthesis is going to be made canon; talking to people with green Matrix code running down their bodies for an entire game would get real old real fast).