What is the purpose of the Immortal trait for custom rulers?

You're correct - guaranteed 6/6/6 is a tremendous boost to the overall development and progress of your nation. No more 0/1/2 heirs that live till 80, you get +3 adm/dip/mil points more every month for 380 years than any other average nation. You can at the same time rush technology in early game and boost development in your starting province. Also keep in mind that you won't get stability hits when ruler dies. This directly translates to more adm points.

Just don't make him a general and beware of rebels that change government type.

You can actually be pretty smart about it and give the ruler traits as infertile, which gives -2 nation-points per trait (so max -4), and you can make your heir Age 0, giving -24 nation-points, you can then give your consort a trait that gives her -2 nation-points. If you choose the right tiles you can have western tech. By setting your government type to the lowest you save another 10 nation points, and if you don't have an issue with sacrificing some monarch-points you can make your ruler 5/5/5, which is still really good and saves you another 14 nation-points. By doing this you can then go to your ideas, pick whichever ones you like that have a base cost of 0.0, and you will be able to buff 2-3 of those to lvl 2.