If I remember correctly it is the components that you swap out in relation to the cost of the ships original configuration... that is why a cargo ship often can refit to allot of other ships if the same size as long as they use the same engines and number of engines as the engines are such a large cost of a cargo ship.
Example 1.
A cargo ship might cost 1200 BP of which 1100 are the cost of the engines, armour, crew, engineering etc. So this ship only replace cost of less then 10%
If you take you brand new missile cruiser and you fir new engines that is a large part of the ships cost you might not be able to get that within the 20% limit if the engines of the old ships is more than 20% if the ships cost.
For refit you don't want any single type of component that need to be replaced in one single go to cost more than 20% of the ships total cost. This can usually be more problematic the higher up in technology you get with some components as some components such as engineering, crew, hangars etc don't scale in cost while many other do.
The steep cost is also intentional as since you add so many components you pay a hefty extra price for each of them that the final cost becomes huge... you are not suppose to refit a container cargo vessel with fleet carrier and get away with it without paying the price for such fooling endeavours..