Hi again jrartamendi,
Manchester
I don't have experience using the RFM69 (or SX1231) with Manchester encoding (not modulation). I normally use the RadioHead library to access the hardware and I'm not sure if the Manchester encoding is implemented on the library. Saying that you should be able to change it directly on the RFM69 Registers, but again this would only change the bit encoding, you still need to have the same frame format, frequency and radio modulation to be able to talk with another device.
Not Compatible
I haven't spend much time researching but I never see any other user being able to talk with ZWave devices using a RFM69 radio.
Side-effect
It's important to understand that if both radios, ZWave and RFM69, are transmitting on the same frequency, they can cause interference to each other. The fact the can't talk to each other does not exclude the fact both devices will try to "talk" the same spectrum.
Saying that, you can easily change the RFM69 frequency, you normally have a wide range of options. For the 868MHz modules you can basically chose a frequency from 862MHz to 890MHz, as well the frequency bandwidth.
If you have some ZWave devices, try to get the exactly frequency they run and the bandwidth... to avoid interference just move up or down - make sure you stay within the legal frequencies in your country.
Network/Mesh
It'll all depends on your code. You might not be able to replicate exactly how a ZWave network works but you can implement any kind of code to handle packages and route it as you wish. Have a look on the RadioHead library Managers: Router and Mesh (
http://www.airspayce.com/mikem/arduino/ ... index.html).
I personally prefer to use simple topology, specially because the RFM69s have an excellent range and normally don't need routing or meshing, so a central base station working as gateway to another network or to the Internet via a RPI is enough. But yes, you might have situations where you need to go over an obstacle like a big hill and a router linking both sides on the hill would be the only solution.
The only other approach I normally recommend is to use "pooling" for low-power devices. Those devices that can't spend much time waiting for messages to preserve battery. The pooling can be linear, random or controlled by a master. Again, it'll depend on the solution to define the best approach.