The main answer is already present in the question. The complete wording of the hadith is:
أرأيتكم ليلتكم هذه، فإن رأس مائة سنة منها لا يبقى ممن هو على ظهر الأرض أحد
Nobody present on the surface of the earth tonight will be living after the completion of one hundred years from this night.
— Bukhari and Muslim
Jesus was living on the heavens and not on the earth when the Prophet ﷺ said this, hence the hadith does not apply to him. Secondly a general text like this retains the possibility of exceptions if they are proved from an authentic source. And the life of Jesus is proven from authentic sources such as the Quran and Mutawatir ahadith.
As for the second argument about how some scholars used this hadith to negate the life of Ilyas: The stories about Ilyas and Khidr do not merely say that they are alive, but rather that they are now living on earth. As an example of the stories:
أربعة أنبياء أحياء، اثنان في الأرض إلياس والخضر، واثنان في السماء: إدريس وعيسى
Four prophets are alive. Two on earth who are Ilyas and Khidr. And two in the heavens: Idris and Jesus
أن إلياس والخضر يجتمعان في كل عام في شهر رمضان ببيت المقدس، وأنهما يحجان كل سنة ويشربان من زمزم
Ilyas and Khidr meet together every year in the month of Ramadan in Bayt al-Maqdis, and they perform Hajj every year and drink Zamzam
— Al-Bidaya wa'l-Nihaya
إن الخضر، وإلياس لا يزالان حيين في الأرض ما دام القرآن في الأرض فإذا رفع ماتا
Khidr and Ilyas will remain alive on earth as long as the Quran remains on earth, and when it will be lifted they shall die
— Fataawa ar-Ramli
It is this belief that some scholars have negated because of the hadith. The same argument does not extrapolate to Jesus because Jesus is alive in heavens while Ilyas is commonly believed to be alive on earth.
Also note that the use of this hadith by some scholars is their interpretation and is disputed. Other scholars have accepted that Ilyas is alive have shown ways to explain the hadith (such as the possibility that he was on a sea voyage or somewhere else), but that is a separate topic. So you are using a debated reasoning and are further extrapolating it to a different matter. On the other hand scholars are agreed that Jesus is alive and this includes Al-Alusi (see Ruh-ul-Maani) as he has declared Ijma' on this and has declared those who deny it to be Kafir.