Ok, those are all good reasons to choose Arduino, for some other applications of which this isn't one.
I would also just use an Arduino here, I've got a box of tiny ones (Adafruit feather) which would be plenty for this application, and I'm already familiar with the platform. From bit-banging Neopixels, as it happens.
But for running an incredibly simple cron job on a standing desk, none of these are compelling. It makes perfect sense for someone who knows Linux, and doesn't want to learn Arduino, to just break out a Raspi Zero and do what he did here.
It's air-gapped, so the risk of it getting pwned to mine Monero or whatever is pretty minimal. There are no real-time considerations for an action which happens once an hour +/- a few minutes, and boot-time for an application where the first action is around an hour from power-on is also not decisive.