Doesn't seem like the USKP team are much into this problem as a potential fix in their never-ending and thankless job. Don't even see it listed anywhere in their MBT, either people aren't reporting it to them or they're deleting it as unfixable by them.
Or perhaps there just isn't enough feedback on this issue being an issue being directed to Bethesda in the correct manner. Have to keep in mind that only the long term modding community is really concerned about this. Most average gamers are like "Skyrim? That game is old."
I'd like to think that Bethesda would actually address this so modders will have the tools necessary to create immersive content that will extend the shelf life of Skyrim just like mods did for Morrowind and Oblivion and FO3 and FONV...but I dunno. Bethesda has quite often shown that it really doesn't give a crap once they feel all the money that can be made, has been made.
That's because it's an engine problem. Nothing USKP can do about it without knowing assembly and reverse engineering concepts. If I do end up fixing it, or Bethesda ends up fixing it I'll expose it to Papyrus, I already know the functions used.
DEFINE_MEMBER_FN(SetExpression, void, 0x0059DB90, UInt32 type, float value);
DEFINE_MEMBER_FN(SetPhonome, void, 0x005352D0, UInt32 type, float value);
DEFINE_MEMBER_FN(SetModifier, void, 0x005352A0, UInt32 type, float value);
DEFINE_MEMBER_FN(SetCustom, void, 0x00535300, UInt32 type, float value);
DEFINE_MEMBER_FN(Reset, void, 0x0059E320, float value, UInt8 unk1, UInt8 unk2, UInt8 unk3, UInt8 unk4);
The functions themselves are relatively threadsafe since all they do is flag some numbers. These exact functions are used by the MFG console function. Like I said, the functions themselves are not broken. The thread that catches the changes stopping doing whatever it needs to do. SetExpression and Reset still work in 1.9. Modifier appears to be broken, I never tested the others.
How I would go about fixing it would be to place a Read/Write trace on the related flags in 1.8 runtime, then set the modifier to find out what reads the flag and probably replicate the process in 1.9 to see the difference.