It just slows down PCA access and make text hard to read when the server is set to 16-color driver. With hundreds of domains, list boxes just don't work. There is no reason to load 10,000 keys at start-up. Load the keys on first request. That will help you sort out the dynamic config part that you said is troubling you.
Users can now edit the error messages for their domain without administrator intervention.
You should caution them, however, to keep the files under 2k in size. Additionally, a sample was included with HAL demonstrating how to redirect from a HAL page to a larger page. HAL wasn't intended to. It's been stated that there is a strong demand for custom error pages, but there are wild variations in features wanted. A look at the feature set in iEP gives you some idea how varied it can be.