Those are not real issues , Djibouti which Ethiopia already has a rail link is at sea level, Djibouti also has multiple airports that heavy cargo can land and be transported via rail, it will even give a boost to their SGR which is also facing similar first time challenges like Kenya.
Besides, If what you are claiming is true, how come Ethiopia airline is the second biggest in terms of cargo transport, and all of it goes through their hub at bole airport, How comes Ethiopia airlines flies to over 60 destinations far and wide on every continent. Does that mean big body aircraft will transport their cargo to JNIA and then smaller aircrafts will airlift them to Addis Ababa? Is that even financially sustainable? If the problem is stopping and refueling b4 landing in Ethiopia, how is that worse than using extra fuel to pass Ethiopia all the way to JNIA, offloading the cargo ,tranfere it to a warehouse, and then another plane with its own fuel come load up the cargo and do several trips and fly high enough above Kenya territorial space. And if JNIA has such advantage over Bole airport and JKIA, how comes JKIA carries half of the Air cargo from this region?
2nd thing if Ethiopia needs bulk Raw materials from Tz, they won't import them by air as that would be unsustainable, they will most likely have to use road or rail, which means the goods will have to pass through Kenya.
But anyway, what you have talked about raw material from Tz is something you've made up, Didn't Magufuli just the other day, banned exports of raw materials in favour of industries being set up in Tz to process those materials, And now you want to claim you've made a deal to supply raw materials for the growing Ethiopia's manufacturing industroes! , Magufuli specifically justifies Ethiopia's deal by saying..... " Being a land locked country, the Ethiopian leader has agreed to start using our port to receive some of their cargo, which will then be stored at the airport depot and airlifted to Ethiopia via the Ethiopian airline,” revealed Dr Magufuli.
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Magu didn't even bother to think of ATCL. The lame agreement should have included allowing ATCL to transport the said cargo to Ethiopia. Ethiopia govt creates opportunities for its airline to thrive, I sujjest you learn to do the same,