I have a similar problem.
My real issue is that there are some preferences that are specific to the project that I would like to set and archive with the project. (for example the processor to use or how much RAM is used for file storage). The idea of putting the preferences.txt file into the project directory allows archiving the preferences properly, but, as mentioned in a previous reply has the problem that compiling for a different platform will now have too many settings. Some preferences like "editor.external=true" do not belong to the project.
A better solution would be to put another preferences.txt file in the project directory that contains only the preferences specific to the project at hand. There already is system level preferences.txt file and a per user preferences.txt file. Adding one for the project taken from the same directory as the xxx.ino file would be an elegant solution to this problem.