Yep, but it's exactly the same way when you start a cook in the wsm when the meat is cold. That's why so many folks report 18 hr and longer butt cooks. I didn't shorten my cooks by cooking less meat. I quit measuring temp at the vent and started measuring somewhere on the grate or using the dome gauge. Sorry for digressing though....
Measure at the grate of your kettle and you'll be messing with the seal of the lid. Besides, it's hard to do if your grate is full. Just compensate for the temp difference and cook more to find out what temps you need to be at during particular stages of the cook.