I have never liked the results of using marker on my hackles. I have tried A-D markers (ArtDesign by Chartpac) Sharpies and and number of 'permanent' markers but always end up with sticky feathers and color that just comes off on my hands while I tie.

On the other hand I have become pretty good at dying small batches in the microwave. I have adjusted my recipes down to just a cup of dye and can easily dye up a dozen dozen or so hackles to order. It's also nice to be able to dye up matched components, for example I might toss in a bit of rabbit fur or some yarn to get color matched dubbing. Once I acquired the basic colors (RIT dye) I can mix up just about any shade I need. Black and a really good dense purple still elude me.

In dying I have also noticed the variation in color saturation you observed. Some of it I attribute to variations in the density/porosity of the material and some to oils as mentioned. Adding some laundry detergent (degreasing agent) to my dye bath seemed to help, however some material just doesn't want to accept color. Turkey biots don't seem to absorb some colors as well as others.