I've saved even small pieces of batting, and stitched them together on my machine. It's been the bamboo batting, and it's very obvious where the pieces are sewn together. So far I haven't used any of those pieces, so can't really say what it would look like under the fabric. I'm afraid it would be just as obvious with the fabric over it.
If I had large pieces, I think I'd go ahead and use the new tape they have just for that purpose. Otherwise, I'm not sure I'd bother saving it... but that's just me....