This issue can be resolved by following these steps,
Change the encryption of the SSIS package to "EncryptAllWithPassword" and change the package passoword by clicking "..." and provide a password and store this password in a document.
Close the package and check if the package asks for the newly entered password while opening the package.
Within the job step, when you try to edit the command line, it should prompt you for the package password. Once you enter the package password, it should add the following switch to the command line "/DECRYPT <password>", where <password> is your package password. The only issue here then is that the command line is not encrypted, but I satisfied for now to have the package working properly as a job.
I was able to successfully execute my package, which includes an FTP upload, with no problems from the SQL Server Agent account by using this methodology.