It looks like the level was not relit after making the scaling changes in those two missions. This has been corrected and redownloading T2Fix 1.26a will fix this issue.
Yes, I believe submitting the DML and re-enabling the script autoloading is the best course of action. Perhaps mentioning this in the mission thread would help as well. I see no reason for a patcher to accomodate for issues such as this, especially when it can be fixed by applying a simple DML.