Three way bypasses are used to temporarily bypass a portion of your plumbing system. It could be bypassed during maintenance or if that component broke down or leaked you could temporarily bypass the equipment so the house would still have water. This works by closing the bypass valve and leaving open the inlet and outlet valve, water is flows to the plumbing fixture. If you close the inlet and outlet and open the bypass the fixture has been isolated with no water flowing in or out but the rest of the house has water flowing as usual.
Years ago water softeners did not come with bypasses built in and it was good plumbing practice to build a bypass around the water softener. We often see UV systems with bypasses installed around them too, so if something goes wrong with the UV service it can be bypassed temporarily. Just about every water softener produced and installed in the last 10 years has a built in bypass. 
So are there any disadvantages to installing a bypass? Yes. We get several calls where a family is having concerns with their water treatment equipment not performing as it has in the past. When we check it out, we find that someone, the family themselves, another household maintenance person or even plumbers have mistakenly opened the bypass and now both treated and untreated water is flowing through the families home. This is why we suggest you do not install bypasses around water treatment equipment or if you do, at least remove the handle from the bypass valve so it isn’t opened by mistake.