> From my perspective, debian successfully unified the developer and end-user centric package manager in the '90s

I think a more accurate assessment would be that both Red Hat and Debian extended their package support through repositories to enough packages that developers often opt for the easy solution and use distribution packages instead of package manager provided ones because it's easy to, and there are some additional benefits if you are mainly targeting the same platform (and to some degree, distribution, if that applies) that you are developing on.

Unfortunately, you then have to deal with the fact that some modules or libraries invariably get used by code parts of the distribution itself, making their upgrade problematic (APIs change, behavior changes, etc). This becomes problematic when using or targeting a platform or distribution that provides long term support, when you could conceivably have to deal with 5+ year old libraries and modules that are in use. This necessitates multiple versions of packages for a module or library to support different versions sometimes, but that's a pain for package managers, so they tend to only do that for very popular items.

For a real, concrete example of how bad this can get, consider Perl. Perl 5.10 was included in RHEL/CentOS 5, released in early 2007. CentOs 5 doesn't go end of life until March 2017 (10 years, and that's prior to extended support). Perl is used by some distribution tools, so upgrading it for the system in general is problematic, and needs to be handled specially if all provided packages are expected to work (a lot of things include small Perl scripts, since just about every distro includes Perl). This creates a situation where new Perl language features can't be used on these systems, because the older Perl doesn't support them. That means module authors don't use the new features if they hope to have their module usable on these production systems. Authoring modules is a pain because you have to program as if your language hasn't changed in the last decade if you want to actually reach all your users. Some subsert of module authors decide they don't care, they'll just modernize and ignore those older systems. The package manager notice that newer versions of these modules don't work on they older systems, so core package refreshes (and third party repositories that package the modules) don't include the updates. Possibly not the security fixes as well, if it's a third party repository and they don't have the resources to backport a fix. If the module you need isn't super popular, you might be SOL with a prepackages solution.

You know the solution enterprise clients take for this? Either create their own local package manager repo and package their own modules, and add that to their system package manager, or deploy every application with all included dependencies so it's guaranteed to be self sufficient. The former makes rolling out changes and system management easier, but the latter provides a more stable application and developer experience. Neither is perfect.

Being bundled with the system is good for exposure, but can be fairly detrimental for trying to keep your user base up to date. It's much less of a problem for a compiled language, but still exhibits to a lesser degree in library API change.

Which is all just a really long-winded way of saying the problem was never really solved, and definitely not in the 90's. What you have is that the problem was largely reduced by the increasing irrelevancy of Perl (which, I believe was greatly increased by this). Besides Python none of the other dynamic languages (which of course are more susceptible to this) have ever reached the ubiquity Perl did in core distributions. Python learned somewhat from Perl with regard to this (while suffering it at the same time), but also has it's own situation (2->3) which largely overshadows this so it's mostly unnoticed.

I'm of the opinion that the problem can't really be solved without very close interaction between the project and the distribution, such as .Net and Microsoft. But that comes to the detriment of other distributions, and still isn't the easiest to pull off. In the end, we'll always have a pull between what's easiest for the sysadmins/user and what's easiest for the "I want to deploy this thing elsewhere" developers.