I agree the simialrties are way too much. I think the substrata is all that is left . The waaxa in that apprently coptic folk song is too similar to be a concidence. Also Waxaa which is a focus marker in somali which isn't found in other cushitic languages makes me think that somali because of its relativ isolation persevered a lot of anicent features of east cushtic. The suffix conjugation thing being found in eygptian is even more evidence.Even what @Shimbiris and others have pointed out about certain pre-dynastic Egyptians strongly resembling Somalis cranially and likely phenotypically in general. I think even this ‘Cushitic substrata’ stuff is likely bs and that this was just the language of Upper Egypt that changed over the course of Egypt’s 4k year history after unification with Lower Egypt and the melding of languages over time. It could still possibly be viewed as a substrata in that sense I guess but not this ‘mass absorption’ of Cushitic speakers as they hypothesize.
A large part of the problem is that scholars use written language and Somali wasn’t written until the 1970s and then you’ve had over 30 years of state collapse so not a lot to work with. They are slowly coming to realize all of this though.
Luckily anicent genetics moves fast. If it was just based off lingustics research it'd be decades before enough evidence was compiled . But with anicent genetics. I suspect we'll find predynastic eygptan samples that conclusively prove the connection within a decade