Africa was known as the Dark Continent then and to some extent, I think it still is.
There are still dreadful atroceties happening in the Congo right now today. Although Botswana sounds like quite a jolly place, at last reading.
Mma Ramotswe in No.1 Ladies Detective Agency - loves Botswana and obviously thinks her village is the only place to live. When considering where God sends the wicked people - to Hell? She reckons it is somewhere like Nigeria!!!

That is because it is the neighbouring country to Botswana. We, in Lancashire are the same about Yorkshire..
I think Conrad was considering his own feelings of helplessness and feeling lost. He had tried to commit suicide at an earlier time, so the poor man was obviously not a little ray of sunshine himself.
Whether he was referring to the heart of darkness in all of us is hard to decide although many novelists have used this as a theme - ie Lord of the Flies. Scratch the surface of any one of us and you will find a savage and a barbarian.....so they say.
There were many books written later - some saying that all the evil in the world was within mankind and that we could rise above that - any of us. Others argued that there were actually evil people (irredemable). That there actually is an identifiable evil force in the World. I used to disagree strongly with the latter, but I have began to doubt that stance now, in the light of some media reports over the last few years.