Assume you have a checkstyle configuration as described in [1], also checking pom.xml files in the root directory of the project, then currently those errors (on the module root) will not be shown by checkstyle in Eclipse, but reported by checkstyle run from Maven.

It is possible to open the project local settings for checkstyle and select the java-sources-checkstyle-check resource set and untick "files outside source directories". However this has to be done on each and every desktop for each and every project.

[1] https://vzurczak.wordpress.com/2016/11/28/checking-root-resources-with-checkstyle-and-maven/