It's difficult this, having spoken to an FL assessor. He said that as players/gk's are allowed to wear black and that the referee's can change into colour, if a referee decides on black and then a gk is in black, it more often than not stays as it is. A Level One referee said to me only a few weeks ago that if he gets a teamsheet and one keeper is in black, he gets them to change the colour to 'charcoal'.
The problem comes lower down as if you're a 7-6/6-5/5-4 candidate, assessors will pick you up on that and dock you marks.
If doing Sat/Sun league and being assessed, you should ensure the GK changes his kit.
Hope that helps