> Many whiskies, especially those that are made on the Scottish island of Isley, have a typical smoky taste that develops when malted barley is smoked on peat fire. Chemically, the smoky flavour is attributed to phenols, and in particular guaiacol, which is much more common in Scottish whiskies than in American or Irish ones.
Other barrels used for scotch are typically fortified wine products, like sherry or port. Occasionally limited releases will be aged in things like ex-rum or ex-brandy casks.
As far as I understand, they don't treat the casks differently to other distilleries.
AGING OF WHISKEY SPIRITS IN BARRELS OF NON-TRADITIONAL VOLUME
http://etd.lib.msu.edu/islandora/object/etd:1059/datastream/...
I suspect that if you plotted the still's throughput as a function of boiling point of the inputs, what you'd get is a fairly broad normal distribution centered on the temperature of the still "head" during the distillation run, with the width of the curve dependent on the design of the still. The upper tail of that curve could easily (must, really) be catching small amounts of substances that boil at 200+C.
0) Horsley (1947) Table of Azeotropes and Nonazeotropes http://sci-hub.io/10.1021/ac60008a002
That said, most of the flavor still comes from the barrel.