I just got my Home Assistant installed onto my Synology NAS running DSM5, and I ran into a couple of problems you described.
First up, I had Python to installed. Another package needs it. So now my NAS has both Python 2 and Python 3 running.
For Home Assistant, I had to do a couple of things differently from the setup guide.
I had to use python3 -m pip install homeassistant to get it installed on the correct version of Python. I also had to enable the “users service”, which was causing some “folders not found” errors I was getting.
For the netgeo error, I too am getting that. For now I’ve disabled the discovery service and hardcoded my Sonos and Plex IPs. To install the netgeo service (and there’s another service nmap for network sniffing), you need to install ipkg: http://rescene.wikidot.com/synology-ipkg
I haven’t done this yet, but will probably try that to at least get nmap installed so I can see devices on my network.