First things first, to dissect your inquiry, we have to understand why Mordred is Arthur's son in the first place. (Because he used to be a nephew before this particular change)
It is my belief that the reason why Mordred is made Arthur's son in literature - and why I detest "Evil (and Abusive) Morgause" trope and its sister trope, "Morgan le Fay as Mordred's mom" - is because Mordred as product of incest is ultimately about Arthur's actions and how that leads to his tragic fall and the destruction of Logres under the religious framework of the Medieval narratives.
Remember that Arthur is a divinely appointed king. Via the Sword in the Stone, Arthur enjoys the rulership of the kingdom through God's providence, as pointed out a couple of times in Vulgate Cycle. That incest with Morgause, especially in Vulgate, is how the Medieval writers justified that collapse of Arthur's realm under the watch of God through the loss of that mandate by his own personal sin, that being willing fornication with a married woman, that unbeknownst to him was actually his own sister.
This is why having Arthur be the victim of trickery or having Morgause/Morgan being evil to him through Mordred is antithetical to the purpose of Mordred being Arthur's son. Because doing so absolves Arthur of the moral responsibility of siring Mordred, which would leave the Fall of Logres an unjustified fate for Arthur. If Arthur didn't commit incest, then Logres wouldn't collapse and Arthur would be free to war against Lancelot indefinitely.
Mordred's incestuous birth also conveniently explains why he would even betray Arthur in the first place. In the medieval mind, his improper birth means he is morally deficient in some capacity, leading to a predilection for evil. This was a handy way for Medieval writers to give Mordred an understandable motive while avoid giving him a sympathetic characterization (because I imagine Medieval audiences wouldn't want to feel sorry for the final villain. Notice how there's little material on Mordred's personal adventures outside of a couple of adventures in Vulgate)
With that out of the way, here's my assessment:
- Options #1 and #2 is the standard medieval romance tradition model. Not much to say since that's what I've expounded upon above. Although I do admit a preference for Arthur and Morgause to be full siblings instead of half-siblings.
- Options #3 and #4 I would heavily discourage. Why would you need to have Morgan as Mordred's mother at all? Morgan already has Ywain (and potentially Morfydd) for a child, so you have potential complexities already installed into her character without involving Arthur or Mordred. If this is to rationalize Morgan's clash with Urien, then this is unnecessarily convoluted; there ought to be alternative ways to go about that feud without dragging Mordred into the mix.
- The same goes for "Morgan disguises herself as Guinevere". Unless she was Uther's direct daughter (which would require a significant overhaul of the narrative), I feel you are attaching an inappropriate parallel with Uther to Morgan's character. And again, this idea absolves Arthur of culpability for the incest.
- Option #5 is the stance of the Welsh and the Chronicle Tradition on Mordred. All of my comments before hinge on the presumption of adhering to the religious subtext of the Medieval sources. This would not apply if your project aims for a more secular/agnostic interpretation of the legends. In that case, there's little need for the incest approach. Mordred can remain Lot's son and his motives could be more grounded in politics and intrigue.
