The Marvel Transformers US verse was initially part of the Marvel verse and then it wasnt. At least thats how i think i remember it.
The appearance of Spiderman and the inclusion of the Neo-Knights in the broader Marvel Universe pretty much sealed the deal that they share space...or at least they once did during the Bronze Age of comics. Modern Age has officially wiped licensed properties like Shogun Warriors and Transformers clear of the regular Marvelverse.
The "omniverse" is literally everything that exists in all of creation across all of space and time and every reality and fictional franchise there is. So, uh, yeah. The omniverse "contains" the multiverse of Transformers, and the multiverse of Marvel Comics, which have occasionally overlapped.
Or maybe "across all space-times" since "all of space and time" could be taken to mean all of just one space-time bubble.
Speaking of wiping out licensed characters...this is kind of a side bar but they did actually kill off Hostess Spiderman. https://crustula.files.wordpress.com/2014/11/hostess-spidey-rip.jpg