I have noticed that outputs from HandBrake CLI and HandBrake GUI is different.
I use the same preset (H.265 MKV 1080p30) with both.
HandBrake GUI version: 1.2.2 (2019022300)
HandBrake CLI version: HandBrake 1.2.2
OS: Windows 10
HandBrake GUI Activity Log:
https://pastebin.com/2RxtTkkb
HandBrake GUI File Properties:

HandBrake GUI Codec Info (from VLC):

HandBrake CLI Activity Log:
https://pastebin.com/KEZMt6cA
HandBrake CLI File Properties:

HandBrake CLI Codec Info (from VLC):

If you need any other info to help me out please let me know!
I just really want to know why there is a difference in the output files when I use the same preset.