I think the intermediate station is now getting closer.  I'm now much happier after removing the dual main line past the goods yard.  The goods area now feel sufficiently separate from the running line(s).

Over the weekend, I started cutting/modifying baseboards, and after physically seeing the lack of separation between the hidden lower line (dashed on the illustration) and the line of the visible trackwork, I've realised that a viaduct is not viable, on the basis it will require low boards to accommodate it, which means I wouldn't get proper access to the hidden track in the event of a problem.  Instead, I will make it an embankment with lower ground at the front.  This also, happily, allows for a headshunt without having to worry about a double track viaduct.

It also reduces complexity, removing the need for a single and a double slip, with just one double slip remaining.

In addition, I think this track layout makes for interesting operations.  With no direct access to the Goods Yard from the Down line (Down is right to left), an arriving goods train can either reverse into the Goods Yard from the single track section adjacent the headshunt, or it can enter the station "wrong line" and cross into the Goods Yard through the turnout and the diamond crossing.

Finally, I believe this layout will make signalling simpler.