A person who is davening Maariv on motzoi Shabbos 50 minutes past sunset, and his custom is to prolong Shabbos for 72 minutes, or longer, should he skip ata chonantanu in SE, because once he says this prayer, his Shabbos is automatically over and he fails to comply with the mitzva of tosefes shabbos? (Even though he is not doing melacha, but nevertheless saying ata chonantanu ends Shabbos) Should he recite the first three brachos extra slowly in order that his recitation of the Havdalah will take place after 72 minutes?
He should not skip ato chonantonu, because the halacha is that we are supposed to say havdalah in maariv shmona esrei. It is obviously better to daven after your zman, but if the person didn’t or couldn’t, he is allowed to say havdalah even before shabbos is actually over. It is true that before a person does melacha he should say boruch hamavdil, but saying boruch hamavdil does not mean that the person’s not doing melacha is like not doing melacha during the week. The Shulchan Aruch even says that when a person has a strong need, he may even daven maariv and say havdalah, even though it is surely still shabbos. I am not aware of such an idea that he should daven slower in order to specifically say ato chunantonu after 72. See the following post http://dinonline.org/2018/10/07/followup-to-rabbein-tam-question/