My Nightmare Fastback in .357sig came new with 2 Wilson Combat .40cal 9 round mags. They work flawlessly but do not fit flush with the mag well. Does anyone know of a mag that does?

Since the Wilson Combat magazines work flawlessly in your pistol, have you reached out to Wilson Combat to see if they have a different magazine base plate/pad that will meet your needs?
Perhaps something specified/marketed as "flat" or "low profile" would be available?

Unless that mag is ejected in the pic above, it would appear to have a longer tube than the standard and would still hang below the frame with a flat base plate. I have Tripp research Cobra mags and a couple Mecgar mags for the same pistol, but I bought mine with the extended bases specifically to make them easier to use.

This site has Mecgar and Metal form options for what you seek. I don't have any experience with either, but Mecgar is always highly regarded.
https://gunmagwarehouse.com/al...911-magazines/40-s-w

Okay, I have to admit my ignorance here and beg the question...

why did your Sig pistol come with Wilson magazines?
Why did it not come with Sig magazines?

My best understanding is early models shipped with 8 round Sig marked mags, but were switched to the Wilson mags from factory at some point. I don't know if the originals were malfunctioning or if there were supply issues or what the reason behind it was. I'm honestly not sure which mags my gun shipped with. I'll have to check that out.