Hooking into SharePoint server-side

Please note I am talking of injecting my code into SharePoint server-side (via a package / add-in etc) as opposed to using Microsoft.SharePoint.dll or web-services to access SharePoint.

So my problem is this, I need to customise how Document Libraries work, including custom permission management. I have been browsing through Microsoft.SharePoint.dll analysing the internals of its working. Here are my observations:

SPDocumentLibrary provides the core logic of managing a document library. However, its not a WebPart in itself.
The actual web part rendering for a Document Library probably is handled by ListViewWebPart or a derived class.
There's actually a SPPictureLibrary class which makes me assume it might be possible to inherit SPDocumentLibrary class to provide custom behaviour on a Document library.
WebPartAdder.SiteWebPartGalleryProvider in some way is connecting SPDocumentLibrary to its WebPart inside Microsoft.SharePoint.WebPartPages.WebPartAdder.AddSources method.
Now all this is client-side, none of this happens on SharePoint server itself (afaik). However I see overridable methods on SPSecurableObject that SPDocumentLibrary/SPList override, specifically:

CheckPermissions
GetUserEffectivePermissionInfo
GetUserEffectivePermissions
EffectiveBasePermissions, etc.
What I really want to do is be able to override CheckPermissions / EffectiveBasePermissions on a SPDocumentLibrary inside SharePoint server to inject my custom logic.

I would now divert my research to SharePoint server side dlls and understanding them. But I would love to get some expert opinion on whether this is feasible at all / pointed in the right direction. Microsoft's hallmark (especially considering ASP.NET 2.0 / ASP.NET MVC as a benchmark) is extensibility / provider framework. They provide excellent providers for "things" out of the box but you can create your classes by inheriting/implementing something to replace default providers. So:

1.)  Can I inject into SharePoint server-side. My ideal solution would be to create a SPDocumentLibrary derived class (server-side), and inject it in so that anytime a Document library is instantiated, my class object is created (instead of SPDocumentLibrary, assuming that's the class server-side too. I still need to "reflect" SharePoint server-side classes).

2.)  If 1) is a nopes, can I create a custom WebPart to use a SharePoint Document Library in a way where it gives a native Document Library feel, but still allow me to use a SPDocumentLibrary derived class when that web part is accessed (please again note, all my discussion is around SharePoint server-side, i.e. my code executing inside SharePoint's address space/w3wp process).

3.)  Why do we have logic in SPSite.EffectiveBasePermissions at all. I mean its supposed to be CSOM, and it should simply be responsible for serialization/deserialization of what is returned by/sent to server. However, I see elaborate logic in this overridden property revolving around permission deducing.

4.)  If both 1) and 2) is a no-op (literally :)), do I have any option manipulating SharePoint effective permissions while operating in SharePoint's address space before SharePoint takes any action based on those permissions.

I know its been a long question, but hopefully I am doing my research well.