Lot 40 is not, to be sure, pure malted rye, but it definitely has some malted rye in the mashbill. Old Potrero is indeed all malted rye, and has a distinctive flavor. Lot 40 is the only other whiskey I've had that shows the same flavor, albeit certainly not as strongly. So, from that I deduce that malted rye has a distinctive flavor of its own, distinct from the flavor that unmalted rye brings to straight rye or rye-mashbill bourbon. It sure seems to me that some chemical change in the grain as a result of malting changes the flavor of the resulting spirit.
Regarding the barley in Irish whiskey, I have never side-by-sided Bushmill's Malt with other Irish whiskeys, although I have had it and it seemed to me pretty similar to Lowland SMSW (which tends to be lighter than other SMSW), and did not show the flavor component which I believe to be the unmalted barley. If we ever end up in the same place at the same time, that could make for an interesting tasting experiment!