My first impression was similar to yours, but after re-reading the entire chapter I'm thinking that we're just reading it wrong. Admittedly, it is clumsily written. Some of the assumptions we make due to the original warp travel rules from the core book further complicate this, so just try to forget what was written there (except for the 12x real time vs warp travel time passage, which I'm going to keep).
Simplified, here's what happens during a warp voyage:
1) The GM determines the actual time the journey will take.
2) The navigator tries to determine the same number and the risks involved in the journey. He may be wrong about either.
3) The ship translates into the warp.
4) The navigator locates the Astronomican.
5) The navigator steers the ship. His skill at this will determine the actual duration of the voyage. Now this is the important bit and the one I think you're reading wrong. The result from this roll changes both the GM's actual time estimate AND the navigator's estimate by the same factor. For example, if the GM determined that the trip would take 10 days and the navigator determined 20, but the result of the steering roll doubles the length of the voyage, the GM's new value is 20 and the navigator's is 40. The important part is that this knowledge is available to the navigator immediately. Once he starts steering the vessel he becomes aware that his original estimate was wrong and may inform the captain about this.
6) Potential warp encounters.
7) The ship leaves the warp. Once again, this is a part I think is being read wrong. To see if the ship is off course you compare the GM's duration with the navigator's duration. Nothing else is considered. Since both these values were adjusted by the results from table 2-4, things are more predictable than you might think. If the navigator correctly estimated the length of the journey in step 2 (my steps, not the book's), the GM's estimate and the navigator's will be the same regardless of the results from table 2-4, which means the ship arrives precisely on the target. If the navigator's original estimate was wrong however, the result from 2-4 can have an effect. To continue with my example from above, the difference between the GM's (adjusted) value of 20 vs the navigator's (adjusted) value of 40 means that the ship arrives in half the time the navigator expected (ironically in the time he originally estimated), which means the ship is slightly off course.
What this means is that an unskilled navigator will often give wrong estimates, journeys will tend to take longer, and translating back into realspace will be inaccurate. A skilled navigator will often give correct estimates that end up being wrong in the end because he ends up being able to steer the vessel better than expected, but this will have no adverse effects as long as the original estimate is correctly made. Crushing the navigator roll, to use the phrasing in the original post, has no negative consequence with a correct estimate.
Thematically I'd say that the skilled navigator is capable of taking greater risks with confidence, bringing the ship faster to its destination. This speed comes at a price, since mistakes are more dangerous. The overall effect should be that warp travel is unpredictable and dangerous, but having a skilled navigator on board the ship will let you get to your goal faster than the competition.
One sentence in the Accuracy of Re-entry section on page 34 says: "If the ship exited the Warp early for any reason, it is always severely Off-Course." Make sure you don't misread this sentence! It doesn't say that journeys shorter than the original estimate are always severely off-course. It refers to those unusual situations which force you to leave the warp before the navigator says the journey is complete. It's only natural that such re-entries are nowhere near where you intended to be.
Plying the warp without a navigator does indeed seem very, very dangerous with this system, but keep in mind that these rules are written for journeys through the Koronus Expanse, a notoriously unstable area of space filled with warp storms and far from the Astronomican. When traveling through "friendlier" areas such as the Calixis sector, I'd probably reduce the modifier to the final translation roll dramatically.
Archelaos, you mention warp hallucinations and that they happen every time. I don't see this in the rules, and I don't see how this would kill off your crew. These hallucinations only affect inexperienced player characters and important crew NPCs (which in my case would be one or two NPCs at most). The rest of the crew can be handwaved away and handled only through the Omens mechanic. The section on hallucinations even says that experienced warp travellers are less and less likely to be affected. My overall impression is that these hallucinations will mostly be a minor problem that will affect player characters once in a while, and they are likely to go away early in the journey anyway. If you're seeing something here that I'm not seeing, feel free to elaborate.