there is no way to execute Checks in different configurations. Checks are configured the same for whole launch (on whole project, ....)
you can play with multiple configurations and multiple launches of checkstyle over your code. That configurations will use filters/suppression to skip undesirable violations on certain set of files. That set of files should be base on filename/path. We do not have ability suppress base on annotation.
another approach is to have one config, certain Check have multiple instances in configuration (that are different by "id"). You need manually suppress non desirable Checks in certain file by "id". If class of type A , you do @SuppressWarnings("typeB, typeC, ...").