Winchburgh is an issue, but not entirely unsolvable. The main issue is the pond to the north of the tunnel on the down side, where the water level sits above the level of the track. During heavy rain, it overwhelms the drainage and overflows onto the track and downhill through the tunnel. The pond isn't in railway ownership, but should have something done to it when they get around to building the new houses in the village.
Whether or not Winchburgh itself validates the building of the Almond Chord is debatable. Personally, I'm of the opinion that 'diversionary route' is not a valid reason to open a railway, however, in combination with capacity constraints, it's is absolutely a contributing factor.
The building of the Almond chord allows Winchburgh to happen, by making the timetable much simpler. At the moment, if you built the station, you'd screw up the timetable for the whole central belt trying to squeeze in a stop to serve it. Post chord, there's a lot more slack and leeway in the pathing around Waverley, so improvements like new stations or increased services can take place.