Are transfer transaction fee and mosaic levy always extra?

I mean, is it always NOT included in transfer amount and require some extra funds?

In my use case I need to transfer all funds out of address. So, I need to calculate fee and subtract it from transfer amount, don’t I? And the same for mosaic levy, if any exists, isn’t it?

Yes. Levy is extra fee payed automatically to address choosen by mosaic creator. It can by set to XEM or any other mosaic.