I tried running it with a relatively current version of OpenMW as well. I could exit the monastery by finding a specific spot behind the gates that allowed me to activate them but the tavern was completely bugged because the scripted events did not work and every one was sitting above the chairs if sitting at all.
I was not able to progress any further, I'm not sure if you were because I don't understand what you wrote in parantheses.
Maybe some of it depends on the MW script extender, which would be relatively bad news. Another possibility would be that the vanilla engine simply accepted faulty code that OpenMW does not handle well. I think that can be tested but I don't know how, somehow you can get the script compiler or something to tell you what's wrong with the code.
I'm sure that faulty code or dependencies on Morrowind bugs are a major part of the current incompatibility.
Another difference to vanilla Morrowind is that Arktwend uses the FPS optimizer, if I remember correctly, though that shouldn't matter. The .exe file is probably changed, which could lead to some problems.
You are out of luck and I don't think anything substantial is going to change in the coming years if there is not a large number of modders and programmers who want to make Arktwend compatible or even an OpenArktwend, something I'd wish for with only free assets, -both possibilities are very unlikely, though, since even OpenMW has a very small number of devs who stick around.