How to render and store a color gradient in a ramp texture for 16bit dataset?
It may be easier to compute the gradient on the CPU, even with 16bit precision the CPU can grind out a texture quickly. Then just upload that to the GPU as an image. Also, it doesn't sound like users will be able to pick a new color set every frame so its sounds a lot more natural to have a work flow of: Pick colors -&gt; Generate Image -&gt; upload to the GPU -&gt; use new palette to render.
Are the picked colors RGB choices? If yes then it does make sense to spread the color palette out as wide as possible (maybe even more then 16bits) 65536 pixels is just a drop in the bucket. And a nice wide color range could lead to less banding in the final image.
At some  level the code will have to narrow the range down to whatever the current precision is. If that is the table, and the table has 65536 positions, then the table might contain a lot of repeating colors, but it is easy to compute the table with a new range.