Not a single person completely opinion free towards their own country's politics. If he favors trump's enemies that simply means they don't get fact checked (how things were), you can't over fact check, trump's every single tweet could (and should) be fact checked, he has nothing to worry about unless Twitter interprets his tweets for him. All they're doing is providing more information about disputed facts. Worst case: "Twitter doesn't like Trump so they provided links that dispute with what he said so that his followers have all the supposed facts before they make a decision".
It doesn't need to be transparent,unbiased or fair. Twitter tries to make it so in order to keep and expand userbase.