Most Depot flags were made of wool bunting with sewn cotton cloth stars. (Bunting is a lose weave material, cloth has a tighter weave). Madausís information is spot on, I think your confusing several deferent 2nd National flags for one set standard. Presentation flags, ones not made for a depot, but home made or made special by a flag maker, could have been and where made of silk, cotton muslin (bunting) or whatever was available.
If your making a reproduction of a Mobile Depot 2nd National, use Madausís description on Confederateflags.org but if your making a generic reproduction without an original to go on, cotton bunting will work nicely with cotton cloth stars and lettering.
P.S. the next time to chat with Richard, tell him Tom said hey.