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But: don't we already use GPLed tools, or have the commandline tools all been rewritten in MIT code? Because if some GPL tools are already included, there's no objection to using the GPLed AAC encoders, right?
That depends on how the AAC encoder is linked to other code. AFAIK code is not forced to be licenced under GPL if it dynamically linkes GPLed code (GPLed code is provided as an add-on or a shared library). If it statically links the GPLed code then the source code has to be GPLed as well.
The Media Kit uses add-ons for encoder/decoders, right? The hypothetical AAC encoder add-on would statically link the AAC encoder, and would have to be GPLed. The media server and other apps, that load the AAC encoder add-on at runtime, are not forced to be GPLed.