The Thelio Mira shown in the picture above is a prototype and is missing the 1u cutout for the bottom PCIe x16 slot. Your Thelio Mira will have this slot cut out.
The BIOS Flash button is not needed when performing UEFI firmware updates via the System76 Firmware Manager. Use of the BIOS Flash button is not recommended.
The upper HDMI and DisplayPort ports will only work if your CPU supports integrated graphics (for example, the AMD Ryzen 3 3200G or Ryzen 5 3400G.) In most configurations, you should use the display outputs on your graphics card if one is installed.