Has anyone else run across this "anomaly"? I can update the price level that has a discount percentage off of the base price using the UI or a script. For example: Base Price = $100; 50% off price level = $50. On the UI or a script I can change the 50% off price level value to any number like $40 which then doesn't make it truly 50% off the base price.

this seems like native behavior, you can change the item rate to any value regardless of price level. It's also possible that your rate and amount fields do not match, ex you can set the item rate to $5.00 set your quantity to 2 pcs, which should set your amount to $10.00 but it would still let you modify that $10 to something like $25 while still keeping your rate at $5. common customization is to lock the rate and amount field on UI.