In my (one and a half) years of experience, I've concluded that no one is at fault for pooling. Yes, dyers can dye in shorter sections, or perhaps use more colors or fewer colors. Knitters can alternate skeins to attempt to remedy the problem. Unfortunately, you may still end up with a final project that you're unhappy with (and if you're unhappy, so is your knitter).
To me, it seems to be a compatibility issue. Sometimes your beautiful hand-dyed yarn is just not compatible with your pattern. Take, for example, this beautiful hand-dyed yarn (by Vedilli Yarns). This sat in my stash for a while and I finally had a project for it - testing the Crunchy Mama Slouchy Tam for Knoodle Knits. I thought it would make a beautiful, bright hat for my daughter. Everything was going well until I began the increases... and then things got bad. Really, disappointingly bad. I loved the pattern and I loved the yarn, but combined, they just didn't work. If I wasn't testing, I would have increased or decreased stitches to attempt to get rid of the pooling, but testing is all about making sure the numbers work, so I couldn't do that. I considered switching yarns, but I couldn't find something else suitable in my stash (I know, this is hard to believe!). I stuck with it. The final result wasn't horrible, but it was definitely disappointing.
It really could have been worse, I suppose - and when worn by my daughter, it really looks just fine. Still, I was disappointed in the final result because I felt like I didn't do the yarn justice - and when I'm knitting hand-dyed yarn, I really feel it's my duty to make the yarn look as beautiful as possible. This may not be a goal for everyone, but it certainly is for me. If I want to show off a stitch pattern, I'll use a nice semi-solid instead.
Anyway, fast-forward a few months. I was supposed to knit a pair of shorties for a charity auction, but of course couldn't get my act together in time - I got them halfway done and they just weren't up to my standards. I pulled the rest of this lovely yarn out of my scraps pile and decided to knit the fastest thing I could think of, a newborn hat.
We still have not answered the question of the hour though - who do you blame if you send something off for a custom project and you're not happy with the pooling? Honestly, I don't think you can blame anyone. The dyer does not know what project will be knit with the yarn that they dye; they have no control over what it does when it is knit. The knitter will likely do her (or his) best to make the final garment look as nice as possible, but it's difficult to achieve perfection, even when alternating skeins, increasing/decreasing stitches, or changing needle sizes.
My recommendation would be to be flexible and honest. If the knitter shows you a progress picture (which hopefully they will) and you are unhappy with the way it's pooling, tell them. They don't want to knit an entire garment and have it sit in a drawer in your child's room because you're unhappy with it but were afraid of hurting the knitter's feelings. Be open to suggestions from the knitter, and hopefully the final result will be something that pleases each of you - or perhaps if the yarn wasn't quite right for the project, you can find another pattern for your beautiful hand-painted yarn.