I guess I really love to see sparkly marking lines on most temari (for a gal that wears no jewellery - except my wedding ring - I sure love my temari bling) so I love to leave those marking lines on the temari. If it looks good I leave it.
I find it very difficult to ignore 'inconspicuous' threads, they just never seem to fade into the thread wrap for me. I have tried matching Perle 8 or a thin embroidery satin thread but they are quite obvious. I find using two wraps of the base thread just hopeless as I tend to stitch more at night when the lighting isn't as perfect as it could be. There was a time when I would have been too scared to remove my marking threads for fear the whole temari design would explode off the surface. These days I am more confident about the security of my stitching (nice thick base thread layer and I ensure I take a good bite off it with my needle at every stitch) and as I understand the divisions better it is easier to remove the marking threads I don't want to leave on the ball. If the design calls for having inconspicuous marking threads I am usually inclined to mark with a contrasting sewing (serger) thread and just remove it at the end.
I guess we all do what we like (and feels comfortable for us), and as our experience grows so does our safety zone. This means we all eventually amaze ourselves when we realise what once seemed impossible (or daunting) has become a part of our regular routine... and we hadn't even noticed.