Actually you typically apply for citizenship after you become a permanent resident, and it takes less effort (from the candidate, at least). But in any case, it is the same service that is in charge of both citizenship and permanent residency, and they are understaffed. Perhaps they will give more priority to Startup visas processing than to other types of visa.

Permanent residency is the major step towards canadian citizenship, and the biggest bottleneck. Citizenship is (from what I heard) relatively straightforward after waiting the necessary number of years.