Rob,
A partial and incomplete response to your question.
The majority of the local units raised for the Boer War were categorised as Class C. From
this document
it seems that Class C were raised in South Africa for general service in South Africa. Units include Brabant's Horse, Canadian Scouts, Damant's Horse etc. They reported to the AAG, Colonial Forces.
I would imagine that their class, in addition to the geographic areas, also dictated the length of service range, pay rates, applicable regulations etc.
Class D1 could only serve in Cape Colony. This sub-division is limited to the Cape Colony Cycle Corps and Settle's Scouts.
Class D2 could only serve in particular districts of Cape Colony. Examples include Border Scouts, Namaqualand Border Scouts and Bushmanland Borderers.
SAMIF encompassed Class C and D. The Town Guards, DMTs and Rifle Associations were not part of SAMIF. Units existing before the war were also not SAMIF, eg Kaffrarian Rifles, SRV, CMR etc.
To add a little confusion, SAMIF is both the name of a QSA-issuing unit and this umbrella term for units raised during the war.
I would be interested to learn to what Class A and B refers. This could be regular regiments of the British Army perhaps?