The heat loss rate due to different methods are interconnected.

it is not possible to only hinder one particular method of heat transfer, so we can never hope to really compare differences due to just one method

the thermometer acts a sink of energy and cools the water as it absorbs heat from it to make the measurement of temperature

The temperatures of the control and experiment cups are not the same as time goes on and so the rates of each means of transfer would actually be different