This is a system-wide preference. It seems like it should be per project. I don’t want my php projects defaulting to python files. I have to go into the preferences for each file and change the indentation settings. If file type was per project, that would not be necessary.
I agree that it makes sense to be able to set a default language per project. For now I recommend using New File from Template, Ctrl + Shift + N.
I’ve filed an enhancement request. Unfortunately that is a “nice to have” request and will have a low priority. For now there are more important tasks to be completed.
If you use New File From Template you will work-around the issue you’re experiencing where the default indentation setting is different per file type.
Remember, you can skip around dialogs using Tab and Shift + Tab when you’re choosing the language template to use after pressing Ctrl + Shift + N.
A workaround is fine with me. It beats changing every file I create!