I think it might be a mixed blessing.
In the west, yes they have more territory, but suddenly there is an outside threat that might help rally the Latins around the Latin Empire in Constantinople. Picking that fight could get messy, especially if Venice gets involved.
In the east, there is Trezbizond, who to be honest is relying on Georgia for its survival at this point (and a beefy Georgia too), but will likely become vassals as per OTL. There might be more controversy as they are now the only claimant to the Roman throne that is Orthodox, which might see some loyalists/restorationists head that way to seek shelter or provide support, boosting them a little, but I don't see it making a massive difference.
What I do see, is a stronger Sultanate subduing Trezbizond, and then spending its energies in the east against the smaller Turkish states, before it (as per OTL) getting hit by the Mongols.
When that causes it to collapse - what I can see is that with the Latin Empire in the West, and the Orthodox Trezbizond in the East, that the period of peace under Seljuk rule will have seen Trezbizond do very well, with an increase in Orthodox immigration from other parts of the Seljuk Empire. Which leaves them in a position to take Northern Anatolia, whilst a more unified Latin Empire takes advantage and invades Western Anatolia (killing the Ottomans in the Crib).
Sadly, the Seljuks were doomed IMO by the Mongols. Therefore unless they can become strong enough to hold them off - anything they do will be to the benefit of whoever can take advantage of their collapse. In this case, a stronger Latin West and a resurgence Orthodox North. All in all, with their state constantly exposed to the Turks, I can see the Romans in Trezbizond being more tolerant of Turks and Sunnis, not to the point of conversion, but enough that if they expand they have more understanding and willingness to allow some self-rule whilst using them as auxilaries to the Greek and Georgian forces. Throw in extra support from being the only Orthodox Imperial claimant, and they could do well - and create a new Byzantine Empire for a new Roman Era. (Which, inevitably, historians will dispute, AH forumers will dispute too, and switch between Roman, Neo-Byzantine and Chaldian Empire)
