Lovely quilt ... now to get it to the finish line!
I know what you mean .... contrasting thread is easier to see for the quilter,
... but matching the thread is nicer, to let it fade into the background.
Some thoughts on thread ... try Invisafil 100 wt. It disappears even if it has some colour to it.
Doesn't solve your challenge of "seeing" it because you want to stay dark.
Possibility? a dark purple ... might give a wee bit of contrast, but might also fade into the black?
Take a look at your lighting ... move things around from your normal set-up.
Can you get more lighting aimed at the quilting area?
Perhaps set up a floor lamp? I'm thinking more of an industrial/work lamp, than a household.
You'll figure it out ... I am sure!