Considering the plays that Yami Marik made by fusing/unfusing with Ra was actually not a legal in-game move, (actually fusing then using de-fusion to separate) he can probably fuse with other characters in the context of the battle, as the Rod makes the cards real.
Really weird things happen depending on how you view those illegal moves.
For example,
Marik can't just go into Ra form whenever he wants. He has to have the rod, then start a shadow game, then actually summon Ra ingame, then he fuses with Ra, and the shadow game makes it "real".
If the fact that he is already in Ra form implies that the whole thing is taking place in a shadow game (because that's the situation in which he can be fused with Ra), the the JLA team is screwed.
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