The Navis Prima listed on page 146 indicates that it's a chart outlining safe routes through the warp, but for some reason the listed bonuses for a good- or best-quality specimen apply to Navigation (Stellar) tests. Could this be an oversight?

Yes, the description contradicts itself, I ruled it applies to naviagtion (warp).

Anonyrnous said:

Same here.

Given that it is stated that uncharted regions of the Warp give a -10 or higher to Navigation rolls, I Houserule that the basic quality Navis Prima allows travel through the Warp at no penalty, and higher quality ones give a +10 or +20 bonus.

This works on the assumption that for a well-mapped area of space like the Calixis sector a library if Navis Primae will be available for the whole sector, thus accounting for the standard Navigation rolls. The dangers of uncharted space thus become that much greater.