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I have a question regarding the meaning of a verse in the first part of Dua.

"O Allah, let your peace be on Muhammad the chosen and on Aly the Favorite"

If one follows the interpretation that Ali is Allah in the batini sense, how does one interpret this verse?

My question is, Why would I pray to Allah to bless Aly, when they are one and the same?

Dua is a zaheri prayer and it is to be said by everyone from a small child to an old aged, from a person beginning the path to a person advanced on the path (at the haqiqati level) and by Ismailis of all historical traditions. At the basic level, all Ismailis accept MHI as an intercessor and therefore Dua statement that you have alluded to reflects this. Those with the Batuni understanding will have their own way of dealing with the statement.

Otherwise, the statement is a Salwaat which has been discussed under several threads in the Doctrines section bearing the name 'The Holy Salwaat'.

I would also suggest you to read “The Holy Salwaat”.

I think you are mixing Zahir and Batine aspect of Salawat and the versa in part one. You are combining both and getting confuse.

You’re 1st statement “O Allah, let Thy peace be on Muhammad - the Chosen, and on 'Aly favourite” is from zahir sense and you’re 2nd statement Ali is Allah is from batine sense which is making it difficult for you to understand this two statements. Suppose if we are train, zahir and batine aspect are our two tracks, and if both are not balance we can’t proceed towards direction of Faith. For example, In Gujarat gujrathi is commonly spoken and easily understood, in Madras Tamil is commonly spoken and easily understood and if u speak Tamil in Gujarat it’s very difficult to communicate. Similarly if you are in zahir level of faith trying to understand a concept of batine level it will be difficult for you to understand and accept it.

Your question “Why would I pray to Allah to bless Aly, when they are one and the same?” is again an example that you’re mixing both zahir and batine level.

Our Faith is esoteric, meaning batin, meaning there is a hidden meaning to it. Every religious practice, infact, if we think in general terms, then every existence has a spiritual sense to it. But keeping it confined to the understanding of the du'a and in relevance to the first part, it is merely the beginning of the understanding of the hidden messege that reveals itself as the du'a progresses and ends at the 6th part. Once one succeeds in recongnizing the true meaning and essence of the Du'a, the next is to believe in it wholeheartedly and say your du'a everyday with that understanding and passion and let your "Imaan" be strong and steady. Then the question of uderstanding the logic of exoteric wont come to mind.