I’m not really sure how running a relay within Qubes OS itself is supposed to help obfuscate traffic. Your traffic already is obfuscated as much as it can be by Tor, someone who’s snooping on your connection can tell you’re using Tor and might be able to perform traffic and timing analysis, but that’s about it. If you were to route all your traffic through your one entry node under your own control, it will probably make anonymity worse. You’ll have effectively reduced the number of anonymizing hops your traffic goes through from 3 to 2. This makes it easier for an adversary running a large number of Tor nodes to potentially be able to trace and decrypt your connection.
The only benefit I can see to this kind of setup is if you’re running an entry node, and not only do you route your own traffic through it, you also allow allow it to be used by the rest of the Tor network as an entry node. In that instance you might have a lot of outgoing Tor connections and it could in theory be tricky to tell your connections from the connections of others, but even then, timing analysis could likely be used to determine when your node was serving someone else’s requests and when it was serving your requests (since your requests won’t have an initial incoming connection provoking them like everyone else’s requests will).
Personally I wouldn’t risk it. Tor is designed to be solid if used as designed. Trying to make it more solid by going beyond what it’s designed to do is dangerous at best.