The SCPH-90001 revision introduced a major motherboard redesign (codenamed ):

The SCPH-90001 is part of the V18 revision, which was designated as SCPH-90001 for North America, SCPH-90002 for Australia, and SCPH-90006 for Hong Kong. In summary, the SCPH-90001 is the last, most refined PS2 hardware revision.

The later BIOS version often results in faster loading times and better compatibility with late-era PS2 games that might have faced issues on older firmware.

The SCPH-90001 typically utilizes the BIOS. This version is significant because it represents Sony’s most secure system software for the console. Model Differences - ConsoleMods Wiki

What you are running PCSX2 on (Windows, macOS, Linux?)