The issue you're encountering with the base.odex modification being detected by the Android-Native-Root-Detector despite the absence of modifications, seems to be related to the dex2oat command line parameters and the instruction set features used. The logs indicate a mismatch between the instruction set features expected by dex2oat and those defined in the command line. This mismatch could be causing the detector to incorrectly flag the base.odex file as modified. To resolve this, you may need to ensure that the instruction set features specified in the command line are consistent with the actual features of the dex2oat binary. Additionally, the ignored flag --compact-dex-level might not be directly contributing to the issue but could be worth investigating further. It is also recommended to review the configuration of your Xposed, LSPosed, and Magisk modules to ensure they are not interfering with the dex2oat process. If the problem persists, consider updating to the latest versions of LSPosed and Magisk, as they might contain fixes for similar issues. Furthermore, you could try reaching out to the maintainers of the Android-Native-Root-Detector for more specific guidance related to your setup.