Your description is almost right but in a different order.
Here is step by step process:
1. The program generates a random sequence of characters
2. EncryptPad encrypts the sequence with symmetric encryption in gnupg format
3. The program asks the user for the passphrase to decrypt the key file
4. EncryptPad uses the random sequence from point 1 to encrypt the plain text
5. Then the application asks the user for another passphrase to encrypt the result of point 4 again
6. EncryptPad encrypts the result in gnupg format.
No, both steps of the text encryption are independent in terms of IV but the same algorithm and other configurable parameters are used. They are in File/File Properties...
The encryption of the key file has its own parameters in Settings/Preferences/Key file encryption properties...
No, you cannot influence IV unless you change the source code.
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