My Bernina 1230 does everything I want with excellence -- except quilting with a different color bobbin thread than top thread. I will always get dots of one color or the other on the opposite site.
My machine will handle invisible nylon monofilament in the bobbin (I use YLI brand) so, in your situation, I would try that approach. Invisible nylon monofilament requires some special handling, though. For example, you need to wind it onto bobbins slowly so that it does not stretch while being wound. Even with a metal bobbin, it's best to underwind the bobbin. With a plastic bobbin, I would not wind monofilament on more than half-full. This is because it puts tremendous pressure on the bobbin's edges and will distort a bobbin if wound on too tight and too full.