As mentioned, "clean" and "lingering bitterness" are two separate issues, but I do believe that C02 extract provides a more singular/clean bitterness expression than using T90 pellet hops of the same variety. For instance, Apollo or Hercules pellets would almost never be used in a German made helles/pilsner for bittering, but those hops as C02 extract are among the most widely used for the same styles. There are also other forms of hop extract (ethanol, ect) that preserve more of the original character of the hop (and things like glycosides) for those who feel C02 bitterness is one dimensional. That said, this really doesn't apply to the average IPA home brew. Use the product that gets you the character you want.
As for lack of bitterness via extract, most commercial systems are getting far better utilization and 30-35% is not uncommon, especially when using calandrias. I'd bet most 5-10 gallon pots would struggle to get 25% utilization and lack of a heating jacket can allow hop extract to adhere to the sides of the vessel and bind to trub and hop material.