Can I put a flue through a roof?

If the flue is a “proprietary design” supplied with the appliance and roof penetration is allowed by the instructions, then you may be able to do this. This means the appliance and flue has been type tested in this configuration.
But you cannot extend a flue unless it is part of the design.
For example, you can purchase flue extensions for some 3 way refrigerators to adjust the height of a flue, but extending through the roof would not be lawful.
Here we also need to note that Clause 8.1 does speak about flue design, clearances to combustible materials and maximum temperatures.
If the flue does not have a protective fire resistant sleeve, then a minimum clearance from combustible material applies (25mm).