[dmun]

According to code, flue LINER is just that: a liner for a masonry chimney. code says that there is a half inch air space around the liner, then four inches of masonry. The chimney cap on top of the masonry exterior is what supports the vertical flue liner, and if cast in place, is flashed so that the flue liner is a slip fit (for heat expansion) rain leakage is prevented by two layers of flashing. One layer goes under the top layer of shingles or tiles, and leans against the chimney. The second layer is slotted into the masonry chimney, and goes over the top layer of roofing. These flashings can be quite complicated. The reason for this is that the structure of the house can move at a different rate than the chimney going through it, and a rigid connection will bend and break causing leakage.

Now for a freestanding oven, with nothing combustible in it, then you can probably just run the flue tile through the roof and wrap flashing around it, tabbing it to go under the top layer of shingles. Resist the impulse just to slather roofing cement around an exposed flue tile: burning roofing cement isn't a very appetite enhancing smell.