Silks or windings on the saddles obviously aren't ideal. However, I have yet to be able to hear a difference in a mix and would even be hard pressed to consistently hear a difference soloed. Others may have better hearing than I do but I've never found it a problem. I've also never had a problem intonating a string with smooth silks on the bridge. Rough windings on the bridge are a different story and can be a pain to intonate but there are ways to work around those situations.
The silks weren’t the intonation problem; that was just an issue with the strings. The only silk problem was perceived sustain/volume impact. It wasn’t huge, but it bugged me, and I’d rather eliminate things that bug me when I can.
) that it is difficult/impossible to get a very low string action on Thunderbirds with the original bridge. So, I thought I'd give that a go, see how low I could get mine. 
