I am not sure of the spiritual equivalent of the three layers of darkness around the embryo. Especially if you are trying to relate it to the discussion of the parallel between the growth of the embryo and the spiritual growth of a human as expounded by HMGA. The only thing I can offer is that just as physical growth takes place in darkness, hidden from view and is internal. Similarly the spiritual growth is also an internal process, whose true manifestation will be in the next life.

Naseer Ahmad Farooqi sahib (marhoom), in his dars on this section, relates the three layers of darkness to the phrase just before it “creation after creation” and the one after “That is Allah your Lord [Rab]”. He states that there are three creations/stages for an embryo (initial creation in the womb, breathing of the Spirit and birth into this world) and at each stage he is in darkness about the subsequent one. The embryo’s lack of knowledge about the subsequent creation (i.e. inability to see) does not mean that the subsequent stage will not happen. Similarly man also has three creations, one is his birth into this world, then Barzakh and then Qayamat when all are raised for judgment. The lack of knowledge about the next stage (inability to see) while in the previous does not imply that the subsequent stage will not happen. Plus, Allah is the Rab who just as He guides an embryo by developing him through all of his stages in darkness, He will also guide man through his subsequent journey. And just because man cannot see the next stage, does not mean that it will not happen.

I don’t do justice to how he explains it. You will have to listen to it yourself. BTW, the version on the aaiil website actually gets garbled at that exact point where he start talking about this ayat and then ends J …you will have to look for another audio copy of that dars.

“…The primary significance of khalq is measuring, proportioning, synonym taqdir (Lane’s Lexicon); hence khalq comes to signify the mere act of the determining of a thing. The word was used in this sense in pre-Islamic poetry. The act of khalq in the sense of creation cannot be attributed to any being except Allah….”

“He created you from a single being, then made its mate of the same (kind). And He sent down for you eight of the cattle in pairs. He creates you in the wombs of your mothers — creation after creation — in triple darkness. That is Allah, your Lord; His is the kingdom. There is no God but He. How are you then turned away?”

(39:6)

Which verse refers to the three layers of darkness around the embryo?

These verses also show the connection between the acts of khalaqa (creates) and qaddara (measures).

and compare with entry for Kh-L-Q

http://www.studyquran.org/LaneLexicon/Volume2/00000435.pdf

appears that the meanings are very similar when talking about creation.

The ending of this verse “And everything with Him has a measure” is significant and adds to the meaning of the verse.  The word “miqdar” is familiar to Urdu speakers having much the same meaning, and the root is qaf-dal-ray (Q-D-R).  However, the meaning is closely linked to khay-lam-qaf (KH-L-Q) or he created.  The same root of miqadar (Q-D-R) form the words taqdeer; again familiar word to Urdu speakers commonly understood as destiny or fate.  Doctor Basharat Ahmed http://www.aaiil.org/text/books/others/basharatahmad/taqdirpremeasurementislam/taqdirpremeasurementislam.shtml and Khawaj Kamaluddin  http://www.aaiil.org/text/books/kk/riddlelifekismut/riddlelifekismut.shtml have explored this in depth and interpreted that every entity at the moment of creation is created according to a certain measure so that within the entity are placed all the qualities that with proper development and nourishment will enable to fulfill its destiny or goal.  Hence at the time of conception the fertilized egg has within it in latent form information stored in the DNA that will enable it to grow, with proper nourishment from the mother into  ultimately a human being; and without proper nourishment it may not develop to the intended goal.  Now my question is that is the “single soul” referred to in 7:189 the spiritual equivalent of the fertilized egg; an undeveloped entity with all the qualities embedded into it to blossom into the “soul at rest” with divine nourishment.  So that in 13:8, Allah is stating both those that “fall short” and those “which they grow” were blessed with the same qualities to begin with. 

Secondly the physical and spiritual parallel of the development of the embryo as described in the Quran (See 23:1-14) has been discussed by HMGA http://www.aaiil.org/text/books/mga/sixparallelstages/sixparallelstagesphysicalspiritualperfectionlightholyquran.shtml .  Can any one throw light on the spiritual equivalent of the 3 layers of darkness around the embryo mentioned in the Quran? 

http://www.alislam.org/quran/tafseer/guide.htm?region=H1

The above link takes you to the compilation by Maulana Nuruddin Sahib and there is a drop down in the top right corner which also has Mirza Sahib’s compilation as one of the last options.

These may not be exhaustive and sometimes the context within the book or the article where the text is taken from is important, however it is a worthy and noble effort.