No, committed generated code does not invite manual changes. This should obviously be prevented and part of your standard software development process and guidelines. That's why autogenerated source files usually have a big warning in their headers, and you would kill any manual changes in code review with a telling off of the dev, anyway. Very simple to enforce and maintain.
At least you have the whole compiled code base under source control, you can guarantee that you have access to the exact source files used for previous builds, and debugging is generally easier. You have the generated code subject to your normal code review process and everyone can easily inspect it. You also have a separation of concerns and source files, embedding Python scripts into your, say, C files is conplexifying everything for little, if any, benefits.
At least you have the whole compiled code base under source control, you can guarantee that you have access to the exact source files used for previous builds, and debugging is generally easier. You have the generated code subject to your normal code review process and everyone can easily inspect it. You also have a separation of concerns and source files, embedding Python scripts into your, say, C files is conplexifying everything for little, if any, benefits.