In 7.x, themes were allowed to participate in any alter hook because the code that invoked theme alters lived in drupal_alter().
In 8.x, there has been a clear and distinct separation between ModuleHandler::alter and ThemeManager::alter. So now, in 8.x, themes can only participate in an alter hook if it is explicitly invoked for themes as well. An example of this can be seen in ElementInfoManager::buildInfo:
$this->moduleHandler->alter('element_info', $info);
$this->themeManager->alter('element_info', $info);As far as a "list" of what alter hooks themes are allowed to participate in... I really don't know of any. This base theme implements the majority/common alters hooks found in themes and you can see what it implements in bootstrap.theme. The only other suggestion I would have towards this subject is to see what code implements the module alter and see if there's a theme alter along with it.