Is anything lost by removing them? Since the GM just makes all the numbers up anyway, it seems like you could skip a step and say
"Well, in order to take control of the moon, they'll need to secure all shipping in the region, ensure the support of the general populace, and make deals with the nobility. Or at least two of the three, and I'll throw in an extra PF if they do all three."
"Well, Seizing The Moon is a Lesser Endeavor that should require 200 points to complete, with Securing Shipping, Ensure Support, and Noble Dealings each being worth 100 and a bonus PF for every 100 by which they exceed the required total"
Admittedly, a lot of ship components have ingame traits (Barracks, for instance, give a hefty bonus to Military objectives) but it doesn't seem like it'd be too hard for the GM to take note that the players should be a bit more successful at things they're actually equipped to do.
Note that while theoretically this could go in Houserules, I'm more interested in hearing accounts for how using the points system for Endeavors has actually worked out for GMs that've had experience with it, since I"ve seen some accounts of games where players amassed tremendous PF using an optimized ship (If a barracks is +100 Military Objectives, and Military Auspexes are another +50, then completing an Endeavor with two Military objectives would leave the players with 300 more objective points than they need, for a cool +3 PF, in addition to whatever the Endeavor yielded, and that's with a pretty minimal level of optimization.)