MBR/GPT and BIOS/UEFI aren't anywhere in-depth as clock multiplier, bus master/slave or IRQ/DMA/IO.
MBR/GPT and BIOS/UEFI along with SecureBoot are neatly explained in the UEFI and motherboard manuals. Also custom parts imply you're running XMP memory and need to enter UEFI to enable the advertised clocks anyway (Hello! JEDEC).
No jumpers to set for CPU multipliers, IDE master/slave or IRQ/DMA/IO etc.