The android version requires me to select a PIN but it is only 6 digits long? How does the android version of electrum ensure that this tiny keyspace (1 million) stays secure?
The PIN is not used as a master seed in this way. It may be used as an additional source of user-supplied entropy, but the wallet's seed will be generated in a cryptographically secure way, using other sources of randomness to provide sufficient security.
I am unfamiliar with the specifics of Electrum's implementation, but there are generally two possibilities here:
1) the password / PIN is simply used to encrypt the wallet, and is not used as input for the seed
2) the password/ PIN is used as a '13th/25th word' that acts as a password on the mnemonic. Find more info here. Also, from BIP 39:
A user may decide to protect their mnemonic with a passphrase. If a passphrase is not present, an empty string "" is used instead.