What Java actually stores inside Keystore when generating Keys?
Nitpick: keytool accepts both alias and keypass if specified; if not specified it prompts for key password if needed but defaults alias to mykey. A JCEKS file can be operated on either by keytool or by other code. 
JCEKS can support three types of entries: privateKey, trustedCert, and secretKey (the older and default JKS file can do the first two).

The operations and algorithms you ask about are "symmetric" (not "synchronous") and use a "secret" key NOT "public" and "private" keys which apply to algorithms like RSA, DSA, ECC.
Also symmetric keys including AES are NEVER in certificates.

A secretKey entry contains the secretkey encrypted using the keypassword (using a PBE aka key-stretching algorithm). The password itself is not stored, which would be totally insecure, and instead must be provided on any attempt to access the privatekey. Note that you can change the alias of a secretkey entry and/or re-encrypt with a different keypassword without changing the key.