If the .less files of a custom skin mimic the file structure of Vector (styles.less containing @import statements for files in the skins/mystyle/components directory or called "variables"), they won't be loaded. Instead, the files from the skins/vector directory will be loaded.
This is because of the path precedence in $wgResourceLoaderLESSImportPaths. First, the LESS compiler is initialized with the import directories from wgResourceLoaderLESSImportPaths and only in the course of compiling the file from the custom skin, the path of the custom skin is added to the importDirs variable of the LESS compiler.
This behavior breaks the reasonable expectation of a skin developer that the included .less files are read from the skin directory.
Proposed workaround (if no code solution is possible): Put a comment in styles.less of the Vector skin, with a warning to choose a different file names than those of Vector in your own templates.