I find the colors of the highlights too strong and fatiguing, so it is my use to decrease their opacity from the internal Bookends reader settings.
The problem (as you can see from the screens below) is that once I close Bookends the opacity is reset to the initial value of 100%..
I see that Bookends sets the correct color (with opacity) in the PDF. If you open the PDF in Adobe Acrobat you'll see that, too. However, if you open it in Preview the opacity is ignored. This seems to be a limitation of the macOS implementation of PDFKit. So Bookends saves the correct opacity but it's ignored when the PDF is reopened and rendered by PDFKit. I'll dig a bit deeper, but I don't hold out much hope that there's anything I can do about that. The workaround is to use a lighter color and ignore opacity.
It seems PDFKit ignores highlight color opacity when the document is opened, it's something Bookends can't control. You'll see the same thing in Apple's Preview. I've found threads about this dating back years. Who knows, maybe it will be fixed in macOS 16 (unlikely).