I mean, if the words are not included in the BIP39 wordlist, it makes it more secure. Or isn't.
It is neither less secure nor more secure.
The thing to remember is that the words are simply an encoding of (in this case) 132 bits of entropy. The entropy is generated first. It is then encoded in to words primarily to make it human readable and easier to back up. You can encode the entropy any way you like - binary, hex, Base58, BIP39 wordlist, any other wordlist, and so on. The entropy doesn't change, only the way it is represented.
it will use the same encryption method to create the seed phrase but it will be more safer than before, or I am missing something here.
It is not encryption, it is simply representing the same data in a different format. But again, the security doesn't change.
And a question of seed phrase and pass phrase, the phrase you created by giving the wordlist of thesaurus, is it seed phrase or pass phrase? I mean in pass phrase we use our own preferred words. Or I am also missing something here.
In this scenario we are talking about using a custom wordlist to generate a seed phrase. But in general you are right - seed phrases are almost always generated using the fixed BIP39 wordlist, while passphrases are generated using any words, symbols, or strings we want.