As the operators gain experience they plants could be built to handle more variable streams such as municipal or industrial waste.
There's still a whole lot of engineering that needs to be done. Think of it as automobiles in the 1930's or semiconductors in the 1960's...
Since the system outputs are oil, natural gas, purified water, and refined minerals, I can see this being an excellent replacement for sewage treatment plants, along with other types of monolithic biological waste. Tackling more "mixed" waste will be an interesting challenge -- will they be able to keep efficient with an input with a varibale mixture of different types of itmes? From the process description, I'd bet it would work fine -- the "unknown" mix of minerals refined from the process could probably be separated into layers via centerfuge.
Of course, for non-biological (and non-petrochemical) waste, you'll get less oil and gas and more minerals in the output, because it's really only hydrocarbons than can be re-arranged, as far as I understand.
On an interesting note, the company is in talks with auto manufacturers in Detroit to build a plan to process shredded cars. Again, this should produce much less oil and gas than bio waste, but it should produce pure iron and aluminum (and whatever they're alloyed with) to be used in future products. One thing they need to watch out for -- I beleive the electronic systems may use mercury switches, they'll need to separate out the mercury and keep it well away from plant workers.