Why does segregated witness change the tx fee calculation?
My guess: To incentivize users to upgrade into segwit.
That is the carrot, and the raising fees of regular txs, the stick.
This is called discount, eg for the same work (1KB transactions) miners are supposed to get less in fees if it is SegWit transaction within Bitcoin Core.
Fortunatelly miners are free to set their fee policy and hopefully there will be full node client available requiring for the same work (1KB transactions) the same fees whether it is normal or SegWit transaction (if soft fork SegWit gets activated which is uncertain).