As raised by Richard Oelmann at https://moodle.org/plugins/view/theme_flexibase the current implementation of the indentation checks fails badly for theme layout files.

These files are typically HTML files with PHP embedded inline. Normal indentation rules do not fit this situation. Humans readability rules, and should not trigger prechecker error.

For now, it might be best to simply ignore the indentation check for the theme//layout/ files, as suggested by stronk7 in the moodle dev chat.