I suggest to disable sandbox (mimic WEBKIT_FORCE_SANBOX=0) when the application runs in a Flatpak sandbox. The current behavior just means to run a sandbox in a sandbox, which feels like an overhead. I know the "attacker" can get to the application data, but not to the system data, thus it should be fine. More or less. I've got this idea after seeing a Flatpak-related downstream print bug report: https://gitlab.gnome.org/GNOME/evolution/-/issues/1236 which you may or may not consider covered by the bug #202363.
The nested sandbox is intentional. Having only top-level sandboxing isn't enough because you run web content from multiple origins in a web browser, and those origins are expected to compromise the web process and try to hack each other. The overhead should be pretty minimal. I know it's not necessary for Evolution, but it is needed in general.