Madzi, that's a lovely rifle.
Here's what I reckon:
I think the military butt on your rifle indicates it has had a replacement butt fitted at some time.
I think the stock disc is 3rd Battalion, North Staffordsire Regt - or am I mistaken? If so, this battalion did not participate in the South African War.
I've not come across a Boer capture in which Britishunit markings were struck out in this fashion.
As far as destruction of captured Boer rifles having their butts smashed, I think that is an unlikely scenario. I have seen a photo of captured rifles being destroyed by sledge hammer, but the barrels are visibly bent beyond repair. I've also heard of rifles being burnt.
In conclusion:
Being a commercial pattern of a military-type rifle is consistent with its having been purchased by the British South Africa Co.
It may well have been a Raider's rifle.
At some point it's had a replacement butt fitted.
TerryLee, who is a regular on the forum is the world expert on rifles like this, so you might contact him for his input?