Okay, so we've got the "storyline" in one half of the book and the mechanics in the other.
I think of it more as we have a setting portion of the book that is designed to give players and GC a common ground to work from in their expectations: it helps everyone be on the same wavelength when imagining what things look, sound, and taste like, a history that makes the particular set to toys avaialble feel plausible, culminating in a present day which offers 10-12 big ol' plot hooks, some obvious, some sly. Do it yourselfers should be able to read it and gain inspiration. Folks who do not have the time to build galaxies of their own should be able to read it and start a campaign that weekened.
The rules section contains the mechanical goodies. Character options. Technologies. GC support (world building and setting features). Some of it will be precisely tuned to the setting (my smartmatter and associated tricks could be re-skinned for other settings, but it takes it flavor from a particular decision made about how physics in this one works) but much of it will be broadly reusable/adaptable.
Would it be possible to keep them separate?
We pretty much always do, in terms of presentation. As has been mentioned, things that are designed to compliment the particulars of a setting, like master classes, will probably mention things from the setting amongst their prerequisites or targeting statements, but most of our toys are designed to be interchangeable. The quartermaster previewed in S&P is a
Farthest Star class for example, and is handy in all sorts of settings.
As I mentioned before, the Rifts line was notorious for mixing storyline with rules and I hated trying to weed through the "fluff" to get to what I considered relevant.
Again I'll point out what one person thinks is 'relevant' can't be a driving consideration for us, but presenting things in a logical and useable fashion so that anyone can find what they want quickly is something our master editor is pretty diligent about

.
Keep it separate, throw in the rules for a few basic constructions such as power armor, robots, vehicles, aliens and planets, and I *should* have enough to work with to keep me happy without having to look elsewhere, as I have already had to do for material not covered in the Spycraft core book and convert it to the Spycraft engine.
It was always supposed to be a strength of d20 that parts are at least easily addapted if not fully interchangeable. As a particular of the
Farthest Star setting, independent mobile 'robots' aren't real common. They get used for a bit of drone labor under direct supervision out in the Promise (and other frontieer worlds) but they are quite rare in the interior. They also show up a bit on the battlefield, again largely in a support role rather than as independent units. The folks of
Farthest Star are
EXTREMELY twitchy about the prospect of A.I.s and armed ones are right out. Semi-intelligent devices (Xpertise) of various sorts are pretty common though.
I guess a 2 year run is pretty good, but wouldn't you really like to be the next flagship of the roleplaying community? Isn't it about time that Dungeons and Dragons took a back seat to somebody else's brainchild?
Nah. If you set yoursights on that you burn out fast. I want it to be
good and pay my bills (Confucius said something about that

). I'd
like the acclaim of millions, but that's tied far more to some steps entirely outside of the creative process that we just don't have the tools to take.
I think the only structuring that failed me was the introduction of PL5, PL6, etc. It failed me because it was an attempt to take control out of the GMs hands. It was as if Wizards was trying to say, "If you live in a PL5 world, you can't have PL8 technology".
You are in luck there. I DESPISE tech level sorting that reaches across disciplines. I don't mind having more/less advanced levels within a single activity and even using some sort of dating scheme to help with presentation, but to link mutliple tracks (lets say ammo, comupters and farming techniques) is only sensible in a single setting-wide perfect monoculture. It actively opposes having any real diveristy with which to paint your people, much less your aliens.
Last time I fiddled with it, I was presenting a concept and showing what it could do for you when it was in its infancy, evolving, mature, refined, and integrated levels of use within a society. Probably over complicated for a core book, but it's something the .pdfs can explore at greater length.
This is a real sore spot for me because I recently went through their offerings along with a great amount of other sources to try and cobble together a decent set of cybernetics rules to use in my Spycraft game. The next headache I face is the introduction of Psionics.
I'm not sure the chrome stat concept made a clean transition to the new boards, but you might find it a useful framework in which to slot the various individual benefits/devices you are looking at. The d20 Modern system of limits hurt my brain

. What, Con wasn't critical enough in that game??!?
What it comes down to is that I trust myself to design my own settings more than I trust others to come up with a setting to my tastes.
Sure, but many customers just don't have the time to do it from scratch. This is why there is so much call for adventures even though they are single use material. We need to serve both camps, and part of being of value to folks who
do have the time to DIY is to write setting well enough that it inspires even if it isn't adopted wholesale

.