Technically, I believe that you are correct, that the subordinate clause should be "dass ich schneller ALS ER laufen kann," in the context of a whole sentence. But this usage is considered a bit "heavy" even by Germans.
So the native speaker treats it as two separate clauses. 1) dass ich schneller laufen kann and 2) als er. In this context, the verb phrase "laufen kann" finishes the first clause (thought), and "als er" begins a second clause/thought in the same sentence. It goes back to the idea of putting the verb phrase at the end of the CLAUSE, not at the end of the sentence.
This effectively breaks up the one subordinate clause into two separate clauses, so that one can keep the two thoughts separate. Even in English, "so that I can run faster/ than he," (two clauses) reads more smoothly than "so that I can than he run faster" (one connected clause). Spoken German "follows" the first pattern (reluctantly), even though the rules call for the second.