The VSYNC is also modified before being sent to the monitor. It happens 2 lines* after the VSYNC from the CRTC and stay a maximum of 2 lines (same cut rule if VSYNC is greater than 4). PAL (50Hz) does need two lines VSYNC_width, and 4µs HSYNC_width.
The Gate Array VSYNC is considered complete when the 26th line has been processed. Then the Gate Array stops outputting the palette colour black.
The Gate Array uses 2 internal counters to create its CSYNC signal: