Ok, the above article doesn't say directly why the alcohol effect is higher for low carbers, but it does give me some ideas for further research.

For example: I read somewhere that the intestines naturally produce about 1 ounce of alcohol a day by fermentation / digestion. If this alcohol comes from carbs (and I think it does) then low-carb eaters have a lower level of this natural alcohol 24/7. This would lead to lower levels of cytochrome P-450 (an alcohol-destroying enzyme mentioned above), and consequently, a lower tolerance for alcohol. (Just a theory - need to do more research!)