Did I make the right call with this PC for my son?

The second system sounds like the more complete buy. Once you account for the cooling repair and the small starting SSD in the first one, the price gap shrinks a lot. You also got more fast storage, DDR5, and a setup that was running at more comfortable temperatures in the tests you were shown.

For music projects and sample libraries, 2TB of SSD space is a useful starting point. Just make sure there are separate backups for anything he cares about. A drive's health reading is worth monitoring, and it should not be treated as a backup.

I'd be happy with that purchase. The CPU benchmark numbers favor the PC you bought, but don't read too much into one test. Real performance depends on the software and workload, and both processors are capable systems for the uses you listed.

The standout practical difference is that the first PC needed attention before it was ready, while the second one came with a larger SSD and reported lower temperatures. Check the SSD's health and back up important work, but that reading alone doesn't tell you exactly how much useful life remains.

For emulation, I wouldn't expect that comparison to be the deciding factor. For gaming, both have an RTX 3080, so the rest of the build and the games' settings matter too. The PC you bought looks like the better all-around package, not because every task will be dramatically faster, but because it has more convenient storage and didn't come with an obvious cooling job.

One caveat: a 360mm liquid cooler is not automatically quieter than an air cooler. Pump noise and fan curves matter, especially in a room used for recording. If noise becomes an issue, tune the fans and pump, and check temperatures during the actual audio workload rather than relying only on a short stress test.

Also check the audio interface and its drivers for low-latency work. The PC specs are strong, but quiet operation and a stable audio setup can matter more than chasing benchmark scores.

Sounds like you avoided buying a repair project. The first system might have been worth considering if it were cheaper or already cooled properly, but at the likely final cost it doesn't look like a clear bargain over the one you got.