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Good question. At the MacOSX level all application code is checksummed (cryptographically hashed) and so self-modifying code would be detected and might prevent the launch depending on user settings. There are always questions about scripted languages that are not compiled (or dynamically compiled) and what happens then.
That said ... doing this is a plugin folder means it is not directly part of the Sigil application and so would not and is not part of the signed executable process used on Macs. But it could still be detected by some antivirus or security software and might cause a error on some systems.
So technically, I think self-modifying code in a plugin folder may work now, I am not sure it would work in the future depending on how secure the system it is used on needs to be.
Are the fixes in fonttools really needed? Is there some way to have your plugin check if there are important updates to fonttools, and if so ask the user to update it manually. Or somehow host the latest fonttools someplace ready to be installed someplace separately by the user and then ask them where and then use what the user has installed by adding it to the python PATH early in the plugin?
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