Fixing TX Malleability is beneficial to everyone. This *other benefits* - they include giving the ability to introduce consensus changes without hard forking. This is because we are told that a contentious hard fork is a terrible thing. How does anyone know this for sure!?
So being able to run multiple soft forks at once is a bad thing for you? Include the ability to introduce consensus changes without a HF? Source please.
Why does segregated witness change the tx fee calculation?
I don't really have an answer to this question. This might do:
My guess: To incentivize users to upgrade into segwit.
That is the carrot, and the raising fees of regular txs, the stick.
The same sigop and hash limits could, in theory, be used at any block size limit.
Replacing 1 limit with another is anything, but a nice way of solving problems.