jem - as you point out there are a number of default assumptions made in the manuscript. That is a neccessity required by the VAST range of situations/settings/time frames/etc that are possible under the singular heading of Science Fiction.
Nick's first draft of HARP SF was actually a lot more generic in nature. ICE had him go back and ADD more material, to add in more setting elements specifically. The material was too dry and too bleh without the setting elements (sorry Nick, it was the nature of the material, not the author's writing that caused that feeling).
You mention Traveler as being humano-centric. The problem there is that Traveler was written specifically for the Traveler Universe. A specific setting at a specific time frame. Traveler is not a generic system.
In order to show off some of the flexibility of the system, we had to add in certain setting elements like alien races. And for the record, the races came separately from the setting. ICE worked with Nick regarding the races, offering suggestions and feedback. We had already given Nick the basic outline (extremely sketchy) of the setting that we wanted to be the core of HARP SF, and all we had for aliens there were the Silth (or is that Slith - I can never seem to remember) and some unidentified aliens.
If we only put humans in the book, then how would folks who wanted to use it with alien races know how to build aliens. By giving examples, we give a benchmark from which GMs can work.
FTL drive - only one system will be presented in the core rules and that is the LaGrange/Portal system. Yes, it is totally system dependent, but it is also fairly generic enough that it is easy to adapt it to other settings.
For example, the core is 1 LY per day via LaGrange Drive and 1 LY per minute via portal. If we consider them to be our upper and lower limits, you can then create a break down like the following:
Level Transit Time
1 24 hr/LY (1 day/LY)
2 18 hr/LY (.75 day/LY)
3 12 hr/LY (.5 day/LY)
4 6 hr/LY (.25 day/LY)
5 3 hr/LY (.125 day/LY)
6 1 hr/LY
7 30 min/ly
8 10 min/LY
9 5 min/LY
10 1 min/LY
You want to have space travel like in the Starfist books then use Level 4 and require ships to jump outside the system's gravity well (same for jumping back in). And throw in a d10 Light Minute Error to navigation for every 4 LY traveled in a jump for the exit points (if you have read Starfist, this approximates the Beam Constant, and the problems it causes).
You want Star Trek, then remove the Lagrange limitation and use each level as a specific Warp Factor.
You want Star Wars, then remove the limitations as above, and select one or more levels, whatever is appropriate.
See, it isn't hard to change the FTL rules to suit your setting.
But, putting multiple FTL guidelines into the book would only confuse things overall for others. Besides this book is huge enough as it is...
That goes for many things in the book. Some things are done because of the specific setting or just to give us a default (like the default is approximately 500 years in the future).
Now, ICE has barely had any time to go through the manuscript (due to working on other projects), so who knows, ICE may decide to remove the magic references, or it may not. But in either case, it is not really an issue as HARP's profession system inherently supports multi-genre games, as any categories not found in a given genre are automatically unfavored for other genre, and restricted to requiring specific training from a teacher of some sort in order to learn. That will not change here.
We may decide to change the Stun RR or not (side note: the Stun RR in HARP was set at 150 because of monsters - without it, there would have been no chance to ever stun a dragon or other high level monsters. Yes, it made it harder to low level characters, but even a 1st level character had a chance to resist - a tiny chance, but the chance was there).
It all boils down to this --
Science fiction is too broad in scope to be able to create a generic book for it without including some sort of setting material to set a standard. Without those internal standards, the book would be too direction-less overall. You may not use aliens in your game, that is quite alright, but we do have to supply some to show HOW they are done, and how divers they can be for those who do want them, even if they do not want the ones we show.
Fantasy games have a number of built in preconceptions about a standard fantasy world, pre-conceptions that did not need to be explained as fully as they need to be explained in a sci-fi setting.
Will the book please everybody in every way? No. However, I think that we can please enough folks in enough ways to make the game be popular.