I have personal experience with this topic and there are not any downsides to this option. However, you need to have patience and you also need to be aware you will pay more than the cost of your average piece of jewelry straight out of the display case.
When I say you need to be patient, I mean you need to be willing to wait for your piece of jewelry to be created. Since custom pieces are handmade jewelry, you have to be patient enough for someone to actually fabricate this lovely work of art. It does not just happen overnight. However, your jeweler should go over how long it is going to take before you start shelling out cash.
Custom design jewelry is no different than anything else you have custom made. Someone is making something for you specifically and custom designing it to fit your liking. This means it will be a little more expensive than your typical display case jewelry. This is a very small price to pay to know you have a quality, one-of-a-kind piece of jewelry.