Have they actually announced these? Officially?
Yes, but not what type of ships
Ugh.... Hopefully they'll make something not-marine with their lot. Maybe some renegades or IN vessels.
Possible lists, based on the War in question: Combined fleet for Tyrant of Badab, Inq Intervention force, character ships for involved chapters.
SM fleet with marks of chaos?
Sadly, entirely possible, given the war in question.
Lets see. I said the SM offered terms. The Empire accepted. The codexes of the various chapters are the binding treaties by which the SM live. The Empire has the right to investigate and enforce breaches of the codexes. The SM do not have to cooperate with these investigations as the are not under direct control of the Empire which creates suspicion. One man being able to kill billions by his word alone is what I would call too easy and a result of narcissism and paranoia displayed within the Empire! Honestly to understand the pyschological situation of the Empire in 40k do some research on the spanish inquisitions.
SCs are already overgunned for your argued role.
The system defense systems that you are talking about do not include the black stone fortress. They are small one hit defenses. A single thunder hawk will take them down. It is not a ship to ship engagement platform. It is a transport. It has fast speed and good armour. It can take on escorts but almost any other ship on equal terms must envoke a fallback response unless mission requirements dictate they can not do so. Then the SC must rely on its defenses rather than its fire power to complete its mission unlike other fleets.
@Zelnik Here here mate!
Barras, there is only one Codex Astartes, and quite a few chapters don't follow it.
And... I hate to say it, but not a single system defense would die to one thawk. Please check your blue book.
And, sadly, I'm quite familiar with the operations of the 'real world' Inquisition and most of the other crimes of humanity.
And, again, please note that a SDF monitor, an escort, outguns the SC, and is the most likely escort for it to encounter several of. A standard space station is more then one SC can handle on it's own.
It is SO easy to point at the space marines and say "I want more", Mostly because SO many people play them and SO many people love them. It's hard to tell obsessed children that their heroes are not what their propaganda plays out to be, especially when the creators of said heroes stated that everything they write is hit with a healthy dose of propaganda.
For example, Space marines killing a craftworld? Uh, probably not. It was more likely a Haven Spire they invaded.
Actually, it is conceivable to do so with a surgical strike against the craftworlds infinity circuit. According to Planetstrike, if the infinity circuit of a maiden world (the proper term escapes me) is destroyed, within hours every eldar on the planet lays down and dies. If one could do such a thing to a craftworld, it's conceivable that it would meet the same fate.
AS far as your other points:
1) The primary advantage of the IN is how grotesquely they outnumber the SM. Remember that a 2k point game represents the bulk of an entire chapter's forces, but a small fraction of what the local IN can bring to bare. Further, the majority of the time, a chapter of space marines might only be abel to field a handful of ships due to being scatered across several warzones. Even if the SM ships were better then thier IN equivalents, the advantage, at least in the 'real world' of 40k as opposed to the abstraction of BFG, would lay with IN due to sheer overwhelming numbers.
2) True
3) True and false. The major balance is the number of SM ships. Lances would take a back seat to that by a wide margin. No source I can find suggests that the Admech monitor the SM at all other then monitoring their geneseed.
4)True
5)Problematic, as to defy the command of the Emperor is heresy, but occasionally he passed out presents way above what In feels safe with now. And, frankly, how is SO a VBB? It was modified to it's current configuration during the first Tyrannic war. That's only 200 years BCE in 40k. There are frigates more 'venerable' then that.
And, again, you forget that we're looking at the bulk of an entire chapter's forces.
6) Hard to say. Part of attack rating is the ability to formulate strategy, which, unfortunately, their hundreds of years of experience give them an edge in.
7) True, though some may have sworn oaths to do so.

I disagree somewhat here, as there are specialist chapters who are experts in exactly the sort of ship to ship boardings that we're talking bout, and that level of expertise should have some impact.
9)More powerful, probably not, as powerful, sure.
10)That's like saying 'Well, we use this nuclear device for clearing rockslides, but it does a dandy number on cities, too!'
11)Agreed, however, I also sort of agree with the new rule for them only autokilling an escort on a +4