I’ve been thinking about this again recently and while building over the A5 in Omagh initially sounds ridiculous, if the proposed A5 upgrade/bypass ever goes ahead, I could see the A5 between the Crevenagh and Derry Road roundabouts being replaced by the railway as the road loses its importance (ironic considering the road was built on top of the railway). A similar thing could be done with the A5 in Strabane once it’s superseded. This would allow both stations to be nearer to the town centre than would’ve otherwise been possible.
An issue though with the A5 upgrade is that the portion between Strabane and Derry is located on top of the optimal alignment for if the rebuilt Derry Road was to remain east of the Foyle, so it’s likely that the Derry Road will have to follow its original route. That makes a Letterkenny branch easier, but might complicate things with cross-border construction, or if they ever want to revive railfreight around Derry.