Something I vaguely mentioned in one of my previous posts in this thread:
It's only when you merge a list that's been modified by a script that you'll have a dirty save issue with this. As long as no more list mergers are done
after the first time a script modifies a leveled list that's included in the merger, there shouldn't be any problems.
For example:
1. Mods A, B, C change lists directly (i.e., in the Construction Set), so need to have their lists merged.
2. The merged list .esp winds up with merged List 1, List 2, and List 7.
3. You add a mod that uses a script to modifiy List 2: no problem.
4. You add a mod that requires list merging, and that only changes List 4 and List 7. No problem.
5. You add another mod that requires list merging, and this time List 2 is changed.
Now you have a problem: because of the scripted change (in my step #3), List 2 is already in the saved game and the changes made in the merged list .esp (by my step #5) won't be used: classic dirty save.
I no longer have Morrowind installed, so I haven't tested this. However, based on everything I remember about dirty saves and leveled lists, I would be very surprised if the above wasn't correct.

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The above isn't helpful for somebody who already has dirty save problems with merged leveled lists, but it might be useful for preventing them.
1. The simplest approach: if you want to use mods that use list merging
and mods that use scripting list management, just make sure you add all the list merging mods to your game first.
Then be careful not to add any more list merging mods after you've added mods that use scripted list management.
Probably most useful when starting a new game or just starting to add mods to your game.
2. A little more involved approach:
Find out what lists are modified in each type of mod you use: what lists are changed in the mods that need to be merged, and what lists are changed in mods that use scripts for leveled lists.
Then you can add new list merger mods
as long as they don't affect lists that are changed by installed mods that use scripts to modify lists.
For example, if you're using a mod that uses scripting to change List 4 and List 9, you can still safely add a mod that uses merging as long as it doesn't affect those two lists.
3. And a more accurate version of approach 2:
Look at your saved game to see what leveled lists are currently stored in it: those are the lists that have actually been modified by scripts. Then look at mods you want to add (that use list merging): as long as they don't change leveled lists that are in your saved game, you're home free.
(To see what leveled lists are in a mod or in a saved game, you could use the Details list in the Construction Set: just click the left-hand column header to sort on that column, then scroll down to the 'LEVI' and 'LEVC' entries: those are the leveled item and creature lists. {I think; it's been a while, and my memories are rusty: but that should be pretty close.})
It should be possible to write a conflict detecting utility to help with this. Point the utility to a saved game and to some mods you want to add, and the utility reports any conflicts: leveled lists that exist both in the saved game and in one or more of the mods.
This late in the life of Morrowind, no idea if anybody would want to tackle this.

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Also, I saw some suggestions about cleaning the leveled lists from the player's saved game.
The problem with this is that it would very likely break the mod that changed those lists in the first place.
...DT staggers off into the sunset, wondering if he will ever be free of this whole %(&@ dirty save issue...