I was playing with the mod! Fortunately, I still had my original zipped download, so I extracted a new "clean" version of the R1-2 and made a quick run with the same choices, and after importing the new clean save to a clean R3 version, and starting a new game, now I am able to actually see the first 12 scenes that the modded save import had skipped.
Yep that is a known issue by the modder and they said they will try to solve it now that R3 is completed (also the issue when transferring saves from R2 to R3), since I play modded and there is also a pdf WT available I usually have it open in a tab just to check if the mod is doing something it shouldn't do, so when I saw that scenes were skipping (it seems to be only an issue when siding with witches) I played unmodded the first episodes of R3 (helps that I save a lot and usually some save will run unmodded even if rollbacks a bit), and got back with the mod later and did that scene without any issues.
URM I only use on my fav games as last resort to check a variable like I did to show you where the scene was called or when the game have no WT mod or pdf WT and have too many branching and I prefer to know in what waters I'm navigating

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On the serious part. Yes, I'm wondering about why people want the mod, or the Walktrough, you get pretty much all scenes being consistent with either the Hardass or the Fair ruler path.
Yeah that is fair, not really needed (maybe I'm just a bit addicted to control my gameplay and mods hahaha probably due to my slight controlling personality, even my profession requires it aka Quality tech) and I never wait the mod to be available and play unmodded anyway if isn't available at the time this game get on my next update/game to play.
But if it is available is a also my way to help the modder to be aware of any issues with it and make it better, I always use them responsibly not like some that unren the game and other weird things with it with the result of installing the mods incorrectly creating issues that aren't there. Also I always keep the zip installation of last version of my favorite games in case I need a fresh game install.