At some point the info_plist= parameter was added to the BUNDLE class.

Looking at the code I see that this handles only key:value entries.

Looking at the Apple doc, for example[1], it seems that some Info.plist 
entries are not simple key:value pairs. The one linked below is, in Python 
terms, a list of dicts,

    CFBundleDocumentTypes=[ {..}, {..},... ]

Obviously the BUNDLE parameter is a help, but cannot address such uses (and 
should not).

But, what should the app developer do for such a case?

The simple solution would be to invoke PyInstaller in a shell script, 
followed by a statement such as

   cp -f src/Info.plist dist/myscript.app/Contents/Info.plist

Do you see any problem with recommending this in the manual? Is there 
anything in the default Info.plist that could not be overwritten (assuming 
the developer knows what she is doing)?

[1] 
https://developer.apple.com/library/ios/documentation/General/Reference/InfoPlistKeyReference/Articles/CoreFoundationKeys.html#//apple_ref/doc/uid/20001431-101685

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