I changed my mind on this. Modafinil doesn't have the specific problem of caffeine, but it probably has completely different problems.

The goal of polyphasic sleep is to use sleep more efficiently. This appears to by skipping early stages of sleep and only getting REM sleep. Quick transition to REM is a symptom of narcolepsy. Narcoleptics have low levels of orexin and orexin antagonists induce REM. Thus it may be that the procedure reduces orexin levels. But modafinil raises orexin, so it may interfere with the main mechanism.

Anyhow, there's a testable hypothesis: polyphasic sleep reduces orexin.