Well it is possible to have Crossovers be a Transformers brand, which it is, but this ends up moving the conversation along to other things, and they will have to be addressed eventually. Some examples:
Beastformers are a part of Transformers, but Battle Beasts are not. Beastformers and Battle Beasts are in the same franchise.
There are Transformers toys in Choro-Q, KT Figure Collection, Super Collection Figure (SCF), Revoltech and MyClone, but those series are not Transformers series. Consider that KT has TFs as well as Getter Robos. Consider that SCF has Henshin Cyborg and Microman in it. Consider that MyClone also has various other franchises in it, and we already know what Revoltech has.
When figuring out Crossovers, I tried to apply the Titanium example to it. As you can tell from the logo, Titanium is not a Transformers brand, but it has Transformers in it. It also has Star Wars and Indiana Jones. But for some reason Crossovers can be seen as being either a TF brand, or a sub-brand of either Star Wars or Iron Man, etc.
As far as making them appear in both series, that is definately possible. A similar concept is used in your Windows operating system, its known as "linking." As an example, a lot of files are "found" in multiple locations, but they actually exist only in 1 location. So all you need is the ability to have certain franchises appear under multiple options but still only exist in one place.
