Let's see here, Book 3 includes
Revolutionaries #5–8
The Transformers: Lost Light #8–12
Optimus Prime #7–10
Transformers Annual 2017
The Transformers: Salvation
That would leave out:
Rom vs. Transformers: Shining Armor (#1-5)
Transformers/G.I. JOE: First Strike (#1-6 + The Origins of Evil)
Optimus Prime Volume 3 (Optimus Prime: First Strike, The Transformers: First Strike, #11-14)
Lost Light Volume 3 (#13-18)
Optimus Prime Volume 4 (#15-21)
Transformers vs Visionaries (#1-5)
The Wreckers Saga (Requiem of the Wreckers) - Have fun paying for two miniseries you already own so you can grab the extra sized solo issue that concludes the story!
Lost Light Volume 4 (#19-25)
Optimus Prime Volume 5 (#22-25, Annual 2018)
Unicron (#0-6)
Skywarp was a core member of that era's GI Joe books as well.
G.I. Joe Volume 1 (#1-4)
G.I. Joe Volume 2 (#5-9)
Scarlett's Strike Force (G.I. Joe: First Strike, M.A.S.K.: First Strike, #1-3)
There was also a character sourcebook that had a bunch of Transformers in it along with all the rest of the Hasbro cast.
Hasbro Heroes Sourcebook (#1-3)
There's also ROM, Micronauts and M.A.S.K. books that are set in the same universe but don't really have anything to do with the ongoing Transformers story for the most part.