The rule doesn't apply to words with two syllables.
The rule doesn't apply to words with than two syllables.
Does the second sentence work? If it does, does it mean "with more than" or "with less than", or either?
No, the second sentence does not work. The preposition / conjunction "than" generally must follow a comparative adjective or adverb.* For example: "more than", "smarter than", "more quickly than". Also, the preposition "with" requires an object, and the phrase "than two syllables" can not function as an object.
*There are a few other situations in which "than" may be used, e.g., following the word "other". However, you seem to be looking for a comparative form.