Add option to set runtime flags (#2239)

For istio/istio#37202

I was originally going to use env var hacks - we already have similar
for `ISTIO_META` and `XDS_HEADER`. However, envoy runtime vars take the
format of `foo.bar_baz=something`. Env vars do not allow `.`, or really
any special charecters other than `_`, so we cannot easily use them.
Instead, seems better to have an explicit field.

Author: howardjohn