1. The server does not store the 12 word, right?
What server?
We are talking about mnemonic phrases for wallets. The wallet software that generated the seed knows the algorithm, and therefore knows how to convert the phrase into a key or set of keys.
how it can compare and make sure of decryption.
What decryption? Transactions are not generally encrypted. The blockchain is not generally encrypted. The mnemonic phrase is not generally given to you in an encrypted form.
2. Since I can transfer the 12 words from blockchain.info wallet to Electrum
This is because the developers of Electrum know what algorithm blockchain.info is using, and they have decided to implement that algorithm as an option that you can use in Electrum if you want to. However, the developers of Electrum didn't need to implment that algorithm if they didn't want to. This was a choice made by those developers.
Why there is no uniform coding system "algorithm"?
Because there is no Bitcoin Company to enforce any rules. Anybody can write any software they want, and you can't stop them.