Hey,
my Fan Control PCB has arrived and I successfully installed it in my MegaPi. I love how quiet (Silent? =) ) my pi is now!
I observed exactly the same issues as you, too - which makes perfect sense, given the fact we seem to have the same fans. Not a big issue for me though, I will be more than happy with just an on/off script!
Also the LED is very bright indeed, but it doesn't shine through the case - I can only see it when I open the SD card storage, which to me is a plus (can debug it visually).
Thank you for making me aware of this PCB! It took a very long time to arrive but I am very happy with it, as honestly the buzzing was kinda bothering me when playing GameBoy games or watching movies.
EDIT:
I am therefore joining the question - does anybody know a fan which would play nice with PWM regulation? This one definitely doesn't like it.