Mobile application security has been a major area of focus for security research over the course of the last decade. Numerous application analysis tools have been proposed in response to malicious, curious, or vulnerable apps. However, existing tools, and specifically, static analysis tools, trade soundness of the analysis for precision and performance and are hence soundy. Unfortunately, the specific unsound choices or flaws in the design of these tools is often not known or well-documented, leading to misplaced confidence among researchers, developers, and users. This paper describes the Mutation-based Soundness Evaluation ($μ$SE) framework, which systematically evaluates Android static analysis tools to discover, document, and fix flaws, by leveraging the well-founded practice of mutation analysis. We implemented $μ$SE and applied it to a set of prominent Android static analysis tools that detect private data leaks in apps. In a study conducted previously, we used $μ$SE to discover $13$ previously undocumented flaws in FlowDroid, one of the most prominent data leak detectors for Android apps. Moreover, we discovered that flaws also propagated to other tools that build upon the design or implementation of FlowDroid or its components. This paper substantially extends our $μ$SE framework and offers an new in-depth analysis of two more major tools in our 2020 study, we find $12$ new, undocumented flaws and demonstrate that all $25$ flaws are found in more than one tool, regardless of any inheritance-relation among the tools. Our results motivate the need for systematic discovery and documentation of unsound choices in soundy tools and demonstrate the opportunities in leveraging mutation testing in achieving this goal.