The tunnel has been listed since 1986:
http://www.britishlistedbuildings.co.uk/en-210514-clammerclough-railway-tunnel-#.VT-d9vD8sY0
so the listing can't be the result of the current electrification project, which was announced in 2009.
However, as mentioned at the link in #17, listed building consent has been obtained for the enlargement.
May not apply in this case, but EH have been proactive recently in listing railway structures, eg signalboxes a couple of years back, and have at least one in house expert.