Matthew
Certainly here in England I feel that our Foreign Office travel warnings are always over cautious - to be point of scaring travellers away. I generally ignore them as 1000's of people travel to Africa each day and those that survive without a mishap don't make "news headlines"
They have to be over cautious - otherwise they may get sued - especially after events such as Bali bombing.
However, their warnings are correct but it's how much you read into them
** "Car doors should be locked and car windows closed at all times."
I assume they mean when not travelling - would this not apply in your country in a bit city...
"Landmines are still a danger along the borders with Angola, the Democratic Republic of the Congo, Mozambique and Zimbabwe"
Yes they are but I am sure the Overland companies know the places to avoid.
"and of common "armed hold-ups, armed car hijackings, muggings and house break-ins."
Quite frightening - might have happened several times in the last few years to a tourist - again you are travelling with a guide and group - so you are well protected.
"Walking in the capital, Lilongwe, is dangerous, particularly from the Old Town (shops and craft stalls) to the nearby new Capital City (nature sanctuary and embassies) with harassment, muggings and bag snatching being common"
I actually visit Malawi often: "harassment" - I get are the street hawkers constantly trying to sell you their wares...
""muggings and bag snatching being common" - don't carry a bag or in fact have many belongings on display - this happens in any big city
"muggings"
Besides the above Overland companies are travelling through all these countries on a daily basis and would not put their passengers lives in danger - they wouldn't stay in business long if they did.
I did this same route 2 years ago with a friend in our own vehicle and we did not once feel that our lives were threatened in any way.... although things did not go smoothly all the time - it was an exciting and memorable adventure.