With that configuration it already uses only one thread per folder. But it is per folder and this can't be changed. On startup, those 50 folders are scanned in parallel. With a sufficiently long rescan interval Syncthing will then randomize the following scans to spread them out over time.
The scanning is already based on size / modtime, but for a hard disk when things are not in cache that's still a lot of reads to do. (Every file stat is accompanied by a database read too.)