Well, the primus motor character is supposed
to be suffering from nonsensical motivations here. And his second-in-command is a creepy alien we don't know all that well yet, nor do the writers, but they have a vague idea that he's got a misogynist streak. On those counts, the episode only delivers what it intends to.
But yeah, while Scotty isn't the master of his own priorities any longer after the "good" Kirk starts messing with his work, he already makes some odd professional choices at the start of the adventure. Not double-checking for the captain? Not following his orders not to leave the transporter room unattended?