It doesn't have to be equivalent, there just has to be overlap that could cause confusion. Prey the game and Prey for the Gods the game: both games, potential for confusion, therefore they needed to followup or someone else could make a very valid argument that they failed to defend their trademark and it is therefore void. Apple the music company and Apple the computer company got into a battle over the Apple logo: two very different industries and yet trademark was in danger; they eventually settled with Apple computers promising not to go into the music industry. If two major players in their respective, distinct industries can have trouble with trademarks how is it so hard to believe that two developers within the same industry might have the same problem?
Suppose they had said nothing, they knew this other game existed but didn't reach out to point out the possible conflict. Another company sees this, says "I want to use the 'Prey' name and am evil" and sues Bethesda for it. They have a valid case, it now falls on Bethesda to prove that there is no chance of confusion between Prey and Prey for the Gods in court, a thing that will cost them money. By pro-actively reaching out they've done their due diligence, they can't be sued for failing to defend.
Again, they didn't really have a choice, this is unfortunately how trademarks work. I believe Bethesda when they say they attempted to reach out to the developers several times before and after the kickstarter, and it was only when they had been unresponsive for weeks that they sent in the C&D. I say again, I'm pretty sure if they'd just responded to the earlier messages something would've been worked out that solves everyone's problems. This isn't the first time Bethesda has gotten into trouble over trademarks and it won't be the last; they're not even the first company to have to defend trademark against little guys either and they absolutely won't be the last.
