Is this specific to Electrum? I used Core. That may be the difference.
Yup. Electrum's seeds never change, encrypting and decrypting the wallet files will not make a single difference.
I thought encrypting wallet is simply hiding original data, good to know so I don't make stupid mistakes in the future.
Nope. It refreshes the keypool.
is this encrypting method as in BIP39 Passphrase? just like what's on iancoleman BIP39 Mnemonic Code Converter?
if so, yeah I guess it would generate a whole different set of addresses for different passphrases
No. Core doesn't adopt BIP39 mnemoric.
if I started with unencrypted wallet and receive some coins, then I decided to encrypt my wallet
would that mean I will lose (cannot see) those coins that I received earlier when it was unencrypted?
There's a string of letters generated for your Bitcoin Core HD wallet. When you encrypt the wallet, Core dumps out all the used addresses and generate a new string of letter to generate new addresses in the future.
Of course you can still access the old addresses. But you cannot access any future addresses generated by the encrypted wallet.dat if you're going to use the old unencrypted wallet.dat as backup.