It would be worse to treat trans women differently than other women.
Some people object to this usage of "you guys." Some people also object to "y'all." I know someone who dislikes "y'all" because it reminds them of confederacy and slavery.
If there is someone who expresses discomfort with certain words, it's usually best to avoid those words in their presence.
By the way, nobody can be expected to know whether or not a woman they are talking to is transgender. "You guys" should not be avoided for the sake of trans women if it isn't avoided for the sake of all women.