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Yes, it makes a difference. Geometric thickness is what the OP is asking about, while thickness is a related but different parameter (since the embeddings do not have to be the same).
It is not always possible with two colours since an $n$-vertex planar graph has at most $3n-6$ edges, and the red subgraph and blue subgraph are both planar graphs. So, any $n$-vertex graph with at least $6n-11$ edges is a counterexample.