This assumes that active PMF members will bother to join a squadron, given that Discord is so much more powerful/flexible.
I find it so curious that this core game feature - playing the BGS - has no individual player accountability mechanic whatsoever.
How could botting ever be combated?
How could an individual player measure the outcomes of his or her actions with meaningful certainty?
How could pmf's track the work of faction members?
How could 5C behavior by a pmf member ever be clearly identified?
How could pmf alliances ever be validated for honesty in action?
This all seems like intentionally obscure voodoo that severely impacts the playability of the game, and the devs have no means to know if it's 5%, 25% or 90% of the player base are cogently involved in the BGS.
Squadrons and PAFs don't necessarily have to be linked. PAFs can continue as they are without Squadrons, and Squadrons can be made that aren't affiliated with a PAF. Individuals can either join a Squadron and/or associate with a specific or not. None of this stuff is intrinsically linked.
The BGS is everything. Any mission, sale, crime, or trade affects the BGS. This won't change with the release of Squadrons. Individual accountability is recorded by the BGS, and is reflected by the BGS. Players are inconsequential, by design.
The effects of any BGS action have a counter. Neither the BGS, nor Squadrons are intended to identify or restrict botting. That is something FD have to take up.
Even now, after the 'tick', you can check the level of influence your favored faction has. Anyone can monitor the changes happening and react.
PAFs can monitor the overall effect of the groups efforts by following, and reacting to the changes in influence. This data will be even more involved after Ch 4 releases. They have even added states and reactions for Ch 4.
5c efforts can never be seen, except through changes in any given faction's influence in a system.
Validating alliances is never an obvious or easy thing, in real life or otherwise. Some stuff just has to be felt rather than have the info telegraphed to you.
All of the stuff coming increases the playability of the BGS. It may not be the open window to the inner workings of the BGS you seem to require, but the required data is available to everyone. Anyone who earns credits is affecting the BGS. Cogently depends directly on the intent of the player. If the player is just looking for the best paying jobs, does that mean that player isn't playing the BGS cogently?
I honestly don't get your issues here.