As long as you are willing to study how your distribution does packaging, adding a build flag to already packaged tool is actually easier:
You could ask your package manager (or a distro build tool) to point you to the source code and scripts which were used to compile the package, install build dependencies, tweak the build, and rebuild. The hard work starts when you need to maintain your tweak on top of existing package in a long run.
I would rather say that as long as you are using build which is done by 3rd party (such as your GNU/Linux distro and not the author of the original project), rebuilding from source should be possible, since both original project and the builder needs to follow certain protocols and expectations for that to work (using common way to share code, using standardized build systems in a clean way ...). What hurts the open source approach is a case when the project doesn't follow usual conventions as it doesn't expect people to rebuild it and provides static binary builds as a main way to use it instead.
> As long as you are willing to study how your distribution does packaging,
That's how I read the article, as saying "figuring out how to make custom package, is too difficult" compared to grab source, edit & compile.
Author does have a point there.
That said, eg. with Gentoo, iirc you'd have 1 huge download directory with vanilla source archives, and a per-package directory with a couple of Gentoo-specific patches. Perhaps with some config file to determine which of those are applied.
If making custom mods to a package is a recurring task, then it shouldn't be too hard to go through the docs & figure out how to add another patch.
You could ask your package manager (or a distro build tool) to point you to the source code and scripts which were used to compile the package, install build dependencies, tweak the build, and rebuild. The hard work starts when you need to maintain your tweak on top of existing package in a long run.
I would rather say that as long as you are using build which is done by 3rd party (such as your GNU/Linux distro and not the author of the original project), rebuilding from source should be possible, since both original project and the builder needs to follow certain protocols and expectations for that to work (using common way to share code, using standardized build systems in a clean way ...). What hurts the open source approach is a case when the project doesn't follow usual conventions as it doesn't expect people to rebuild it and provides static binary builds as a main way to use it instead.