is it possible to just encode an elf executable using the encoders and still end up with a working 'packed' executable? or am i misunderstanding what an encoder is supposed to do.

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No, because the msfvenom encoder can only encode shellcode. Encoding an PE would be different because it requires a stub (decrypter) and loader. A crypter or packer is what you're looking for.

For a more detailed description of how crypters work: https://www.exploit-db.com/docs/18849.pdf

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