I wouldn't make a restricted donation to a charity unless there was a cause I really cared about but I didn't think the charity behind it was well-run and I didn't know a better way of helping that cause.

I do not consider money to keep a good charity running as "wasted"--if anything I am deeply dubious of any charity which claims to have minimal to no administration costs, because it's either untrue (the resources to manage it effectively must come from somewhere, maybe from the founders' own personal resources) or a likely sign of bad management (they think that skimping on the funds needed to manage it effectively in the name of maximizing the basket of "program expenses" is a good organizational strategy). An organization that I think is well-run wants to spend on its cause as much as possible, but is mindful of needing to spend on itself also. If it cannot spend on itself--to hire good staff, to have good training, to use resources that cost money and save time, to plan its strategy and maintain regulatory compliance, to do whatever else an efficient organization needs to do--how can it possibly have the capacity to spend well on its programs? The money to sustain that charity is providing for its cause to be effectively addressed now and into the future.

"Unrestricted" says that you believe GiveWell is competent to make these allocations correctly between itself and its recommended charities. For GiveWell in particular, if you do not believe they can do this, why do you think they can evaluate other charities' effectiveness? Presumably you want to give to the other charities because GiveWell has told you they are worth it, because you think GiveWell is competent at assessing organizational effectiveness. (For other charities, I would have lower expectations for assessment ability--but still I expect that I want to give to one in particular because it is effective at spending for its cause. There are few causes where you do not have much choice of how to direct your money to affect it. An effective one will be competent at running itself--not perfect surely, but competent enough that I don't think I will do a better job at allocating its funds than it will by giving a restricted donation.)

Also, many people's gut feelings direct them to give restricted donations to avoid "wasting" their money; it's a feel-good option but one that does not help the charity stay around in the long term. People who are more considered should compensate for that by allowing the charity to use their funds unrestricted. I have no idea if GiveWell gets grants or not, but grant support from foundations is often restricted as well; it's much harder to get grants for general operating support. But I won't start that rant here.

(For background, I've been heavily involved in nonprofits for the past 10 years, as volunteer, staff, and board.)