So I have an update to this confounding problem that just keeps getting weirder. It has lead to the identification of what the problem IS, but not WHY it is. I have more questions than answers now then I did before...
So I sprinted through the game again on Easy again, tried some different choices, avoided doing other things, etc, just to see if the bugs would happen again, and of course they did. Utterly infuriated, I left it for a bit and came back to reinstall via Origin. No difference, same problem. Beyond annoyed at this point, I left it for a day or so and came back to it with fresher eyes to see if anything would pop into my head. After a while I got a really stupid idea so I decided to try it. I figured, well, I've uninstalled every mod and tried that, and that didn't work, so what about the DLC's? Aren't they mods of the game, technically speaking? I've already tried a completely fresh install and that didn't work, so why would this, right? So I go into the main menu, and turn off every single BioWare DLC, they have a different icon beside their name in the window. Go to the load the game, get captured for the millionth time by Cauthrien and... it works?! What?! I got in! And I far as I could tell, it works perfectly. Captured in Fort Drakon and Alistair was talking and I had the option to wait or to try to break out yourself. Tried many different companion combinations and they all seemed to work. Didn't want to go too far before I can go through with it working fine, but it seemed to have no issues.
So now I begin the painstaking process of turning on every single BioWare DLC on one by one to see what one is giving me the issue. After a rather long time of trial and error, I finally narrow it down to the Stone Prisoner. I turned that one off, which having every single other one on, and it seemed to work fine and the problem identified. But not so fast...
I wasn't content with knowing that the DLC's were somehow the problem yet a completely clean install still was giving me problems. So I ran yet another new character through the game, this time with Stone Prisoner turned off completely from the start. So no Shale for me. Got to the part before the Landsmeet, traveled to Denerim with Eamon, insulted Loghain, left the Estate, re-entered the Estate, and... no Ghost Loghain reciting the same thing I just heard 7 seconds ago. So that's a great start I thought. Continued on into the next part with killing Howe and freeing Anora. Got to the moment of truth, I captured by Cauthrien and... it KINDA worked...? Yeah, the cutscene loaded with Anora and companions telling Eamon about how the Wardens were captured and how we have to free them. Then the loading screen and I was just... there. In the cell with Alistair and no equipment. No cutscene with Alistair talking to me played, and since my character was no Rogue, I was effectively trapped. However that is not the only strange thing that happened, because there was actually a third person in the cell with us, and it was Morrigan? Just there like everything was normal. She was in my crew that attacked Howe's estate and got caught by Cauthrien, so I guess that fits.
So with at least some narrowing of what specifically is the problem, I decided to try the turning off all the DLC trick again, and once again, it works fine. Alistair talks to me, gives me the choices, etc etc. Turn them on one by one and finally seem to conclude that this time it's Return to Ostagar that is the problem. So now I turn on every BioWare DLC but Stone Prisoner and Return to Ostagar and... no, it doesn't work this time? What? That doesn't make any sense, why did it just work, but not now? So I leave Return to Ostagar off and try as many combos of DLC's as I can randomly try until the thought hit me that maybe it's not actually the DLC's themselves that are causing issues, but rather the items that said DLC's give you? So I turn off Golem's Might, Blightblood, Witchcraft, and Battledress of the Provocateur, along with already having Return to Ostagar and Stone Prisoner off, and Praise the Sun, finally it's back to everything working.
So to recap incase you got lost and/or confused on this "War and Peace" long escapade. I have a problem where the DLC's or the items said DLC's give you for beating them cause my game to spawn "Ghost Loghain's" to repeat dialogue already performed, make it so Fort Drakon is either completely inaccessible and warps my character to stand right beside Eamon and Anora when caught, accessible but with a third teammate inside and no cutscene from Alistair to play causing me to be trapped in the cell forever. Turning off specific DLC's will make all problems go away, however other DLC's with items, like Warden's Keep seem to cause no issues. A clean install still gives me the problems, however installing the DLC's, then turning them off seems to fix the problems...?
So to say that none of that makes sense would be the understatement of the century. None of that seems possible, and yet I can't deny what is right in front of me. Can anyone even begin to hazard a guess as to why this is happening? Is my game copy cursed by Darkspawn taint permanantly or something? That seems about as plausible as the actual glitches and current workarounds.
(If need be, I will do a full reinstall and download the DLC's separately and try another runthrough again if it seems necessary. I would like to avoid this if possible, but I hate letting glitches and weird computer bugs like this win.)