After power on, all GPIOs are in Input mode. At this time, the GPIOs can be treated as high-impedence, or floating. In this situation, the voltage level of GPIO is unknow, and is likely to be non-zero, and far below than 3V3. But since the voltage is non-zero, there will be current, and the LEDs can be turned on, with less brightness.
Once the bootloader is running, it will set GPIOs of LEDs to Output mode, and there will only be two voltage levels: 0 or 3V3.
So, back to your question, the WiFi LED is controlled by the WiFi chip. Only after the WiFi driver is loaded, the GPIO of WiFi LED can be set to Output mode. That's why the WiFi LED has two brightness during booting.
The switch LEDs are connected directed to the MT7531, and has the default power-on mode as LED, which is appearently Output mode. The less brightness may due to LED or resistor problem.
Normally MT7621 u-boot does nothing for PCI-e. But breed will pull-down and pull-up the reset pin of all three PCI-e slots. This is a workaround trying to solve some WiFi card issue. There are indeed potential risks which may causing other PCI-e cards work abnormally.