Comparison between namescpace/cgroup with seccomp is not a good idea. These are intended for different purpose as you explained. Basically you should apply combination of these, that is

1. Filter all critical system calls with seccomp
2. Isolate you service from accessing other process resource using namespace
3. Limit the resouce usage (cpu, memory, core etc) using cgroup

Comparison between namespace/cgroup with seccomp is not a good idea. These are intended for different purpose as you explained. Basically you should apply a combination of these, that is

1. Filter all critical system calls with seccomp
2. Isolate you service from accessing other process resource using namespace
3. Limit the resource usage (cpu, memory, core etc) using cgroup