The taxes will usually be coughulative, but there can be exceptions. For example, I found that the USD5.60 tax for an AA flight did not increase when I added anther leg (scheduled within 24 hours). Then again, AA domestic taxes are so low anyway.… Should one expect to pay the same taxes and surcharges for individual flights as a combination? ….
Maybe just do some more dummy bookings, individually, to check.
You could always confirm your taxes with another agent at the Call Centre.

My experience with Cape Town on calculation of taxes has been rather sub-par.
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