いいえ、できません。異なるトラストストアを使用するには、それらのいずれかまたは両方をプログラムで設定する必要があります。
このpostから以下の例を参照してください:
SSLContext ssl = SSLContext.getInstance("SSLv3");
KeyManagerFactory kmf = KeyManagerFactory.getInstance(KeyManagerFactory.getDefaultAlgorithm());
KeyStore store = KeyStore.getInstance(KeyStore.getDefaultType());
String password = Configuration.getConfig("keyStorePassword");
store.load(new FileInputStream(new File(Configuration.getConfig("keyStore"))), password.toCharArray());
kmf.init(store, password.toCharArray());
KeyManager[] keyManagers = new KeyManager[1];
keyManagers = kmf.getKeyManagers();
TrustManagerFactory tmf = TrustManagerFactory.getInstance(TrustManagerFactory.getDefaultAlgorithm());
tmf.init(store);
TrustManager[] trustManagers = tmf.getTrustManagers();
ssl.init(keyManagers, trustManagers, new SecureRandom());
HttpsConfigurator configurator = new HttpsConfigurator(ssl);
Integer port = Integer.parseInt(Configuration.getConfig("port"));
HttpsServer httpsServer = HttpsServer.create(new InetSocketAddress(Configuration.getConfig("host"), port), 0);
httpsServer.setHttpsConfigurator(configurator);
Implementor implementor = new Implementor(); // class with @WebService etc.
HttpContext context = (HttpContext) httpsServer.createContext("/EventWebService");
Endpoint endpoint = Endpoint.create(implementor);
endpoint.publish(context);