Till now there is quite a long trick that makes it possible to set linked prims phantom.
The other solution that has been proposed more recently by LL to use the not prim feature is unusable as it can impact LI count in a crazy way leading to a build returning to its owner inventory at best.
So why not simply have a llSetLinkPrimPhantom(link number, boolean) ?
PS: If it can motivate LL to add such a feature, simply look at how palms are set phantom on the great Aleymart products = it is a phantom script in each item needed to be phantom as the phantom linked prim trick is not permanent in case of link / unlink. At the end it easily makes tens of extra scripts that could have been avoided on each build.
It also means that this features needs to work on the viewer edit window too.