When Thrawn take command of the Imperial Remnant dose he Get The Allegiance Class and the Secutor class Star Destroyers for he's Fleet roster to build and Other ships that were Available at the time.
Nope.
And now the Second Question is, At the start of Era Three should Byss get Starting Super Star Destroyers Or build them as the GC Progress like having Three of the Vengeance Class Super Star Destroyers (Or more I don't know How many they were) Or (I'm leaving out the Assertor Class because Reasons you know why) The Bellator Class Super Star Destroyers And Executor If just have them as starting Units like Hero units and the Sovereign Class SSD's. And Yes I know you build them keep that or just have one (AKA the Sovereign her self) and The other Vessels ( like having the Perator the Allegiance and the Secutor all in the same Era Until Crimson Empire start) in the Era as building them overtime Or just have some. Dreadnaught out and the Rest You build Overtime again the GC Progress until Crimson Empire start.
None of the above. Your access to SSDs in Era 3 isn't really changing. Yes, there were a handful of them in the Byss fleet, but keep in mind that those three Vengeance classes (for example) exist in the context of thousands of other ships in the galaxy. Representing every single SSD that existed in the campaign doesn't make much sense considering the representation of the other ships is not and cannot be 1 to 1. If you could build the Bellator and Vengeance, that would mean there's 5 different SSDs available to that faction at once.
And now final Question, .... well that one been answered allright so..... oh I know Are you going to make a Model for the Executor Class for Stellaris so people can use the Dreadnaught in the game because THAT would be epic
No idea if that will get that far.
and At some point are you going to make a ICW mod for StarCraft 2 and how would you do it.
I have neither plans nor the least desire to make a Starcraft 2 mod. I've never even played it.