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The effectiveness of a visualization technique is dependent on how well it supports the tasks or goals of an end-user. To measure the effectiveness of a visualization technique, researchers often use a comparative study design. In a comparative study, two or more visualization techniques are compared over a set of tasks and commonly measure human performance in terms of task accuracy and completion time. Despite the critical role of tasks in comparative studies, the current lack of guidance in existing literature on best practices for task selection and communication of research results in evaluation studies is problematic. In this work, we systematically identify and curate the task-based challenges of comparative studies by reviewing existing visualization literature on the topic. Furthermore, for each of the presented challenges we discuss the potential threats to validity for a comparative study. The challenges discussed in this paper are further backed by evidence identified in a detailed survey of comparative tree visualization studies. Finally, we recommend best practices from personal experience and the surveyed tree visualization studies to provide guidelines for other researchers to mitigate the challenges. The survey data and a free copy of the paper is available at https://osf.io/g3btk/