Is it possible to influence which codepages and Unicode ranges that will be included in a font compiled with MakeOTF? It seems that the compiler detects those values automatically by checking the glyph/character set in the font that is to be compiled instead of reading the data from the feature or fontinfo files.
The compiler does detect the values automatically, but you can override them by putting appropriate info in the feature file. Check your feature file documentation, and if it isn't in there, we can bug Antoine....
The next version of the FDK will have such overrides. The current one does not. You are stick with the results of the heuristics in MakeOTF. For the short tem, I suggest a third party tool like TTX to fix values you don't like.