It's very common for applications to replace dlls on windows. One example is Office installs or IE installs. Some apps will inject stuff to existing dlls in order to hook to them. Copy protections inject or replace system dlls for example.
These applications (the office and ie ones) do not modify system DLLs. They run the installers for updates to runtimes which have their own DLLs but they never touch the DLLs directly. These are official updates to the DLLs being placed by official installers.
There may be copy protection which does this, but these are not what I would consider to be credible applications. Feel free to name a specific copy protection that does this, along with examples of system DLLs it modifies. Until then, you're not providing a real example.
System libraries and registry are not unrelated topics since both are areas which are commonly negatively affected by windows application installs.
They are completely unrelated in function, and if you knew anything about them you would not try to make the comparison.
All you're doing is demonstrating that you don't understand Linux or Windows. Citing examples of something which can be done on either operating system does not demonstrate that Windows has a problem. It merely demonstrates that you don't know what you're taking about.