Costs are only going to be realistic once there is the political will to do more than a one-time project. I can see the MML being comparatively affordable compared to other projects given the amount of work, especially if they get around to tendering the later phases as soon as it reaches Wigston.
As I understand it, MML costs are still high, although not entirely due to OHLE costs - and even more so for TRU.
Total costs and timescale are more to do with what else Network Rail has to do or wants to do on the route (bridge replacement, embankment works, realignment, resignalling, station rebuilds etc).
For electrification Network Rail also has a regional frame agreement policy which means the incumbent (SPL I think on MML) gets first dibs on work in that region.
It all went haywire on the NW projects because the regional contractor (Balfour Beatty) didn't want to finish the job after the Chat Moss work (ie Manchester-Preston-Blackpool).
(BB had a huge portfolio of Crossrail work and now HS2 so they weren't penalised for their NW position).
Some of the competition has evaporated since NR cut back on its wiring projects.