The standard convention for counting exercise calories (whether by HRM, online calculator, or in a lab) is to include your underlying metabolism as well, as this is part of the total load on your heart and lungs.
However, when calculating your total burn, yes there is a slight double count - a BMR of 1900 represents about 80 calories per hour. For short intense exercise, the double count is insignificant - probably less than the margin of error in a calorie estimate anyway. For long duration cardio, (2-3 hours) the double count is more significant.
M@L