Manpower is on the side of Seljuks
Fatimids have few natural allies unless they totally ally themselves with the christians
without distraction from Romans , the turks would be able to concentrate all their might against fatimids
The Fatimids do have their manifold so-called da'i states and what could be described as sleeper cells of Shi'a aligned militants. When the Fatimid state was rising, the Fatimids used so-called militant uprisings the harry their Abbasid rivals in the east. The whole early Fatimid system was based around repudiation of the Abbasid Caliphal system and hence attempting to overthrow it by systematic promotion of revolution, rebellion and invasion, much like the Abbasid offensive against the Umayyad. Such a system of sleeper militants and coordinated rebellions were a known topic within the Islamic world for the time.
The use of taqqiyyah and kitman combined with a relatively intricate system of vanguard organization made it such that a state or group of people could utilize these militants to cause chaos and mayhem in the enemy realm.
Supposedly, the founder of the Fatimid Caliphate Abdallah al-Mahdi Billah was a descendent of a millenialist Shi'a who was from Iran. This man, for whom he derived was holding a position that within his faith entailed that he was a 'secret Mahdi or Imam who plotted the return of 'true Islam' and the destruction of the creations of the Umayyads and their kin aka, Sunni Islam. His duty then was to send out letters to different men across the Islamic world who were called Da'i that were in charge of a local area commanding a sort of 'shadow religion/government.' During the Anarchy of Samarra these Hidden Imams expected the fall of the Caliphate. They watched as militant uprisings from the Shi'a-Khawarij Zanj revolt, the Khawarij revolt of Jazira, the Qarmatian wars, the beginnings of the teaching of al-Khasibi and so forth. In such a chaos, it was felt that the old order was collapsing and up from the rotten and evil Abbasids, would emerge a holy realm ruled by semi-divine Imams. Across the world, the weakness of the Abbasid permitted the lessening of traditional punishments upon 'heresy' and thus increasingly, the Taqqiyyah which limited public announcement of Shi'a beliefs was lifted and led to massive uprisings, the likes of which had not been seen since Earlier Islam.
In that world, Abdallah al-Mahdi Billah whose ancestor had moved to Northern Africa to escape persecution, emerged from his occultation and declared for his Da'i that is, his representatives, controlling shadow movements across the Islamic world, to remove their taqqiyyah and rebel against their overlords. This began to increase after under al-Mansur, the Fatimids defeated an internal Khawarij rebellion (which had helped the Fatimids take control in Africa). This permitted the expansion finally into Egypt by al-Mu'izz who conquered Egypt fully in year 969 CE.
This was the culmination of the rise of a Shi'a militant shadow government, which claimed to rule all of the Islamic world and claimed to sponsor the creation of the Assasins, the architects of the Qarmatian revolt and the Da'i states that arose in India and Iran against the Abbasid sponsored Turkic Islamic states. It was in this period of militancy and connection to a vast array of rebel states and insurrectionist movements across the Islamic world, that the Fatimids held the most power and the effective ability to inflict serious harm upon the states beyond it.
Generally, this power of the Fatimids waned upon the rise of the Caliph al-Mustansir (1036-1094 CE), who undersaw a huge decline in the Fatimid Caliphate in terms of their reach and power abroad, as the Fatimids internalized their power. Al-Mustansir was the son of a slave from Nubia and his father was the prior Caliph, az-Zahir who shunned his legitimate wives and their heirs in favor of the slave boy, who was supported by the Fatimid court due to his ease of control. The legitimate heir however, al-Nizar, fled to Iran to be among the Assassins who upheld the older Fatimid system. Meanwhile, al-Mustansir underwent a governmental shake-up wherein an accommodationist stance was taken unto Sunni Muslims within Egypt and a decreasing militancy among the military ranks. This led to schisms, as different sects broke away and refused to promote the Fatimid realm, this included several sects of mystics, who worshipped the Fatimid leadership as deities, such movements while small, were zealous and provided the Fatimid state with its most ardent military forces. The loss of these zealous partisans meant that the Fatimid relied totally on slaves and Sunni Muslim alongside a minority Shi'a population.
At the same time that the Fatimids were deconstructing and rebuilding their identity, the Abbasids found for themselves a new patron in the Seljuk Turks who pushed into the region. The Seljuks countered the recent indecision and fragility of the new Fatimid leadership with a zeal to destroy the enemies of Islam and acquire vast loot in service of their lords and the Abbasid Caliph. It was not a good way to be.
As such, I would say, that 9/10 in a scenario of Seljuk-Fatimid war, with a TL set in 1060, the Seljuk will defeat the Fatimids and drive them out of most of the Levant. The Fatimids indeed can only ally the ERE and that does not necessarily always help them. What matters too, is that their armies lack internal support except from minority populations, namely Christians and Shia' Muslims of moderate varieties, both groups less likely to be regular soldiers when needed.