I think this would depend on the environment. If you live in a dry, relatively flat area and you mostly drive there, you're probably right, marginal difference in road safety.
But if you live in a country that has long winters or lots of mountains, having control over the engine is a integral part of staying safe on the roads.
One of my vehicles even has the tranny cooler and the radiator in one unit and is prone to cracking, leading to running radiator fluid through your gearbox, destroying it. The first thing I did was install an external cooler, as the market was big enough for an aftermarket kit for such a part.
Cars are getting so much worse.
Other than that, it’s far less about logic, and more about the feeling of control and mastery that it gives you. True, this feeling is largely more inefficient and more prone to failure than an automatic system, but that feeling, man; that feeling is just so great!
I also live in a wintery country, with many winding roads, hills and mountains with diverse weather and road conditions. The argument was made that it’s better to drive “stick” under these conditions. However, I’m not sure the argument that manual is better for diverse conditions will hold for long, given the current advent of better AI.
I’ve already seen AI drive in very hilly and adverse terrain in the Hollywood Hills, rife with bushes hanging over junctions and pedestrians popping in and out of parked cars, and so on. Naturally, not much ice up there, but that’s a pretty difficult landscape for an AI to master, and the AI already masters it pretty well!
To be fair, it is a bit older, so perhaps modern transmissions are significantly better, but any rentals I've driven were even worse, though they were lower class cars.