For anyone who is interested. I was surprised that nginx was not offering srv lookups in their free version. I found a module that offered this, however it did not work because of syntax differences in srv lookups on mesos. I adapted this module to force sending a whole srv domain, and tests look promising.
You can find this module for now here, but remember if you have groups in mesos use service=_https._synapse.dev._tcp.marathon.mesos. ('.' at the end) https://github.com/f1-outsourcing/ngx_upstream_resolveMK I have asked if the alpine linux guys can add this in their repository. So we do not need to go through this compiling hasle every time.