Sorry but it's just lazy design, the ideal scenario would be to have have quests that branch, get to a certain point and you can choose whether you want to choose the PvP or PvE option
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It's actually not lazy. For instance, you use a weapon made by tex mechanica to get another weapon made by tex mechanica. The weapon you are tasked with using is subpar in pve, wrecks in pvp. That weapon is TLW, of course, and go figure that they actually thought things out and created synergy. Games don't typically baby you with branching quest choices (at least not in terms of difficulty, maybe preference).