E-M78 did not originate in West Asia. It arose in North Africa and was brought to West Asia by North African migrants. It is E-V13 that arose in West Asia within an E-M78-bearing population. Refer to Cruciani et al. 2007:<quoted text>
Those West Asians who belonged to E-M78 though were not Africans by the time EV13 arose in West Asia. E-M78 migrated into West Asia around 18,000 years ago meanwhile the EV13 marker didn't arise until 10,000 years ago, by the time EV13 marker arose in those West Asians they had as little ancestral connection to the Africans who carried E-M78 into West Asia as modern Europeans do who carry the EV13 marker and as little connection as Central Africans R1b carriers do to Asians. Which explains why European EV13 carriers don't cluster genetically close to North and Northeast Africans just as Central African R1b carriers don't cluster close to European R1b carriers. Different branches with different geographical migrations and chronological origins.
The analogy you draw with regard to R1b-carrying Central Africans also does not apply for a number of reasons.
1 -- R1b-carrying Central Africans do not cluster craniometrically with R1b-carrying Europeans. On the other hand, E-M78-carrying North and Northeast Africans do cluster craniometrically with E-M78-carrying Europeans and West Eurasians in general.
2 -- R1b-carrying Central Africans do not have any appreciable quantities of West Eurasian mtDNA like R1b-carrying Europeans do. By contrast, E-M78-carrying North and Northeast Africans do have considerable quantities of West Eurasian mtDNAs like E-M78-carrying Europeans and West Eurasians in general.
3 -- R1b-carrying Central Africans do not have significant West Eurasian autosomal DNA like R1b-carrying Europeans. However, E-M78-carrying North and Northeast Africans do possess substantial West Eurasian autosomal DNA in common with E-M78-carrying Europeans and West Eurasians in general.
So based on the still existing affinities between the E-M78 bearers in Europe, West Asia and North/Northeast Africa, the E-M78 carriers that entered West Asia from North Africa were not much different from their E-M78 bearing descendants in West Asia among whom E-V13 later arose. They were already distinct from Sub-Saharan Africans.