Same situation here. . Configuration done in HelmChartConfig file and required wireguard packages installed (kernels < 5.6), but backend type is shown as vxlan, from canal Pods... "BackendType: vxlan"... I have reviewed the flannel config inside the component containers and it is not applied...
cat /etc/kube-flannel/net-conf.json
{
"Network": "10.42.0.0/16",
"Backend": {
"Type": "vxlan"
}
}