Industrial robot usage and other manufacturing innovations are a big reason they are leading the industry in manufacturing cost and speed. Other manufacturers are starting to emulate a lot of the things they are doing with structural battery manufacturing, casting big parts, etc. The likes of VW and others are (by their own admission) behind and struggling with the number of parts, amount of manual work, etc. It might not be as automated as Elon Musk would like but it is pretty impressive.
It will be interesting to see what they do with their upcoming cheaper model. He seems to be hinting at the notion that further manufacturing improvements are going to be a big part of that.
That said, then there are niches where the automated THT assembly apparently makes sense and all the NRE costs seem to be offset by lower per-unit costs of the PCB material itself. Prime example is mid-range to high-end home AV equipment (Japanese branded if not made in Japan outright), where the large mostly empty single-sided FR-2 boards with truly ridiculous amounts of obviously machine populated wire-links and discrete THT radial components are particularly striking.
After machine milling them roughly to spec there are employees that angle grind, sandpaper and polish every critical surface of these 10 ton chunks of metal.
It's not clearly shown in this, but the majority of the work is manually adding parts.