The practical difference is that the ecosystem of Linux applications is composed almost entirely of open source software. Consequently, installing something you downloaded from the web is much less dangerous than installing a closed source program on Window, provided that you trust the website.
I agree that the centralized scheme is easier to use in the 80% of cases. i.e. when:
(1) The package you want is in the repos, and ... (2) The version of the package you want is in the repos.
But, when those 2 conditions are not met, installing software is usually harder than on Windows. Additionally, I don't like the very nature of centralized things, even if they are managed by the good guys.
How so? I believe the same principle applies for centralized distribution. How do I know the packer didn't change the code?. The same way I trust repo mantainers I can trust application developers, or any other third party.
And reproducible builds are possible both in decentralized and centralized modalities of distribution. Aren't they?