As TrevorD observed, the sentence is far from clear. No wonder you are having difficulty with it!
By re-casting the sentence, I might make the writer's meaning clearer. For example,
"Since their intentions are likely different, Company A and Company B will not likely achieve anything [in my opinion]."
Or,
"I cannot tell what Company A and Company B intend to achieve, given their different intentions." [or "It is difficult to tell what . . .."]
Or,
"What do Company A and Company B hope to achieve, knowing their intentions are different?"
Or,
"Knowing that Company A and Company B have different intentions, I wonder what they hope to achieve."
Or, in order to keep the notion of anticipation in the sentence,
Knowing that Companies A and B already anticipate their intentions to be different, I wonder what they intend [hope] to achieve."
Or,
"Given that Companies A and B already anticipate their intentions to be somewhat different, what do they intend [hope] to achieve?"