The CTT records will be on 'proper' courses, i.e. the start has to be within so many miles of the finish to compensate for ups and downs, rather than a place to place which could take advantage of topography and wind.
One important factor to remember is that the faster modern records will have the advantage of taking place on a dual-carraigeway, and therefore gaining considerable drafting/sucking along benefit from passing traffic. No, it's got terribly right is it, but that's how it works...
Also, the track type records don't have so much cache (hour record aside) for TT'ers. It's fairly unlikely that most of the proper fast guys would want to have a go at it, hence a slower record time. It's also got to be massively boring riding round for 100 miles.