Many of these issues are addressed in the
GURPS and
D20M versions of the current
Prime Directive source books, and should (re-)appear once they are ported into
Mongoose Traveller.
There is a one-page section in
PD Feds called
Time, the Air Force Tapes, and the Star Fleet Universe which goes into more detail on the source material used to create the SFU. But even during the time of the original series, the "literary interpretation" seen on-screen does not always match the course of events in this universe. (Or to put it another way, the only material from
TOS and
TAS which is allowed to be in the SFU is that which had already been incorporated into the universe when the contract with Paramount was signed.)
For example, it's noted in the
timeline that First Contact with the Gorns saw "two brash young captains shoot first and face embarrasing questions later". But the SFU version of events does not involve the Metrons, who don't exist in this universe.
So far as how this Federation treats would-be members,
PD Feds notes that there is a degree of political and social freedom which such planets must at least broadly adhere to before they are allowed to join the club. And even then, there are several stages of membership (probationary, prospective, associate, and full), each with its own criteria involved before a world can move from one rank to the next.
For example, the Antareans described in
PD Feds are biologically related to the Andorians, but are quite distinct culturally. The shock of First Contact (or, more specifically, the revelation that they were descended from transplanted stock taken from ancient Andor) led to a series of social upheavals. Eventually, an Ataturk-esque military leader took charge and set the Antareans on the path towards Federation membership, but they were only accepted as probationary members after instituting a series of democratic reforms.
And while they would later go through prospective and associate member status, their later bids for full membership have been blocked by the Andorians, as the two societies don't get along all that well. (The fact that the Andorians can get away with this is perhaps an example of how the founding members of the UFP differ from those planets and species which signed up later.)
In terms of military organization, the SFU UFP had distinct planetary fleets which were the primary naval arms of the Federation as a whole prior to the formation of the United Star Fleet. (You can see many of them in warp-refitted form in the three Early Years modules for
Star Fleet Battles.) Over time, as Star Fleet came to the fore, the major planets kept a number of their older ships as "training squadrons". These were eventually formalised into the National Guards, which persist into the modern era.
However, while the first generation of National Guard ships were tactical warp upgrades to old sublight plantary ships, the "modern" NG hulls are hand-me-downs from the Early Years Star Fleet. (This "G-series" is mostly presented in
SFB Module R8, along with equivalent "L-series" ships in other local defence forces across the Alpha Octant.)
And as noted in my last post with the Yeney, warp-capable aggressor planets within UFP space are not technically covered by the Prime Directive, but are instead placed under "protective quarantine" - as in, to protect outsiders from the depredations of the subject species in question.
