The cost per script is exactly the same. But there is usually a fund for 4 or 5 extra scripts that might not work out, because you still have to pay the writer even if you don't produce the episode due to the WGA agreement. Without that fund in the third season, they just had to produce any script commissioned.
Oh, I understand the concept. During the first season, at least thirteen stories were bought and then junked (although one, "Rock-A-Bye-Baby, or Die," was bought back by George Clayton Johnson).
What I doubt is the claim that the staff was unable to junk a single story during the third season. Looking at the writers report from the production week ending 3-29-68, in fact, I know this isn't true. The document lists three teleplays that were finished and turned in, but not produced:
"Shol" (Darlene Hartman)
"The Joy Machine" (Theodore Sturgeon)
"He Walks Among Us" (Norman Spinrad)
It lists several story outlines that were turned in, but not produced:
"Bem" (David Gerrold)
"Down from Heaven"* (Lee Cronin)
"The Godhead" (John M. Lucas)
It also lists several story outlines that were assigned at that point, but not produced (this is the last writers report in the Roddenberry papers at UCLA):
"Van Voyt's Robots" (D.C. Fontana)
"Ears" (D.C. Fontana)
"Japan Triumphant" (Lee Cronin)
"One Million, B.C." (Lee Cronin)
"Shore Leave II" (Theodore Sturgeon)
*Might this be "Let That Be Your Last Battlefield"?