Installing from the openSUSE repos with Zypper provides a native application that is tightly integrated with your system’s shared libraries. A Flatpak is a self-contained, sandboxed application that runs in isolation with its own bundled dependencies.
The native package offers perfect integration with your OpenSUSE installation, while the Flatpak as the nature of being sand-boxed, provides better security by being isolated from your core system. For these two applications (Inkscape and/or GIMP), I would normally go with the ‘repo’ version. Up to you of course.