What kind of CPU does your server have? It shouldn't require that much CPU power to transcode stereo DD+/TrueHD. Unless something else was causing high IO latency, which can inflate apparent CPU usage.
Jellyfin 10.10.6 (Docker)
Ubuntu 24.04 LTS
Intel i3 12100
Intel Arc A380
OS drive - SK Hynix P41 1TB
Storage
3x WD Red Pro 6TB CMR in RAIDZ1 (JF Library)