Yes it is not possible to use the built-in window manager notifications because those belong to KWin, the KDE Window Manager. You can't use 2 window managers at the same time, so when you use Beryl, you lose KWin, along with any feature related to KWin, like notifications.
The only possible "solution" is to use Beryl's sound notifications if it has any and use the KDE sounds for those (you will have to search which ones are which).