Sean
The roof termination on most, if not all hight eff. furnaces allow both sidewall and roof terminations. Generaly when you see the roof termination it was installed when the house was being build, for they have open cavitys to run the pipe. The side wall venting is generally done on change out systems where the origional unit was a much lower eff. system. Hope this helps.

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Well thats my 2 cents.
Brian Kelly
Kelly Home Inspections