Whereas" and "although" are both correct. We can't choose between A and B on the basis of these words.
The reference of the pronoun "they" is unambiguous in both A and B. It refers both logically and grammatically to the subject of the preceding clause "lines." We can't choose between A and B on the basis of this word either.
What makes B wrong is the phrase: "as competing companies one day may be partners the next." The separation of "competing" from "one day" confuses the intended meaning. In A, "companies that compete one day may be partners the next" is clear and logical.