Bundler will always calculate the discount from the actual price and not from the "compare at price." But there is a trick, you can use to not apply too much of a discount on your products.
The trick here is to set a lower discount in the bundle in our Bundler app AND set the app to show the "compare at price" as base price in the bundle widget. You can set this in Bundler > Settings > Use compare at price as base price in bundle widget. This way, the widget will show as it is calculating the price from the "compare at price" but in reality, it will calculate it from the actual price.