Well, after a quick search, from that source, I found that :
…A .theme file is a .ini text file that is divided into sections, which specify visual elements that appear on a Windows desktop. Section names are wrapped in brackets ([]) in the .ini file.
I believe that the themes.txt file has not much to do with the above, furthermore, confusion between the two does not sound a good idea. What is more, one can say that file names such as themes.txt and current_theme.txt are quite descriptive and leave no doubts about their function. However, I think I understand your point of view. Perhaps I would consider renaming these in the future.