Well, if the material costs of refitting are lower than building a new ship, there is your benefit. I am starting to run out of minerals on Earth and if it is cheaper for me to refit than to build new, I guess I'll have to deal with the much longer time frame.
First, what all the other old hands said
Second, you can recover minerals by scrapping the old ships. Don't remember the ratio. So in the situation you describe, I would probably build new ships and either scrap or put into the "reserve" the old ships. (Note that commercial ships like freighters don't cost anything to keep around, but military ships will cost minerals and so are probably better off scrapped.)
Third, as many others have pointed out, the refit system is intended for small changes to the design. For example, when upgrading my conventional-start PDC to TN sensors, I design the new bases with conventional armor and launchers, rather than TN versions. This way, I'm only ripping out the old fire control and putting in new fire control (this is what refit is intended to support). If I replaced everything, I might as well build a new base.
Fourth, a good suggestion to make in the suggestion thread might be for Aurora to launch an "are you sure" dialogue when launching a refit task if the cost of the task is above some threshold (like 50%) of new construction.
John