flatpak: Convert all . after the first two to _

Makes it work properly with the org.kde.okular.kirigami flatpak, currently we got a job called Kirigami_Flatpak.

The appstream id actually seems valid, so we should support it.

"To increase the uniqueness and to distinguish between different pieces of a software suite, it is suggested to append the type name to the component-id in these cases. For example, one can use com.hugski.ColorHug2 for the client tools to control hardware, and com.hugski.ColorHug2.firmware for the runtime firmware files."