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I think that distributions patching software is especially problematic -- whether you consider it a symptom or a cause of fragmentation.

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You're missing the point of free software. You own it and can change it how you like. It's not problematic this is how it was made to be.

Here's two examples of how distros patching software has been helpful for me.

1) SquirrelMail (abandoned) patched to work with PHP 7.3 thanks to FreeBSD contribs

2) Abiword patch builds in the AUR that fix a broken default install.

Is the point of free software to create as much variations of a program as possible?

I'd rather see that useful changes are merged upstream, or projects are forked. If this had happened, you wouldn't even need to patch, and this would save an enormous amount of manpower that is wasted on trivialities.

Distributions exist to provide software that all fits and works together (e.g. providing the correct versions of dependencies). Sometimes patching is necessary to make things work.

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