Correct, Invisafil is not transparent, but it comes in a huge variety of colors. For SID, I find that it pretty much disappears completely into the ditch as long as you pick the correct value.
For texture quilting on the surface, like micro stippling, or matchstick quilting, you would want to match the color to your fabric unless you want to use the quilting to add another layer of color to your surface.
I can't speak to its suitability for long arm/frame quilting, since I am a sit down quilter. I can tell you that my PQ1500s is capable of stitching at 1500 stitches per minute and there have been times when I've had the pedal all the way down and the Invisafil handled that speed quite easily. I have also used it on my art quilts going through many layers of unconventional fabrics and it has done very well in that respect also.
Rob