Different size systems have different bottlenecks, and sometimes you only have to worry about a few of them. I'm trying to think back to things I've done that required understanding kernel behaviour. In the cases I'm thinking of, it's always been some small aspect of the kernel that mattered for what I was doing. So I'd say I have different models of the different parts of the system. If I needed to, I could think about how those pieces fit together to unstand how Linux as a whole works (when running on hardware I know enough about, which for me these days is just AMD64 PCs. I have a vague idea of how highmem on ia32 works, but it sounded horrible so I put that on my list of good reasons to use amd64 and wish ia32 would curl up and die.)
On smaller machines, you have to know e.g. does grep -r on a big source tree start to make your desktop swap out, so the programs you have open are slow while they page back in again. (the answer is yes if vm.swappiness is set to 60 (a common default), so set it to more like 20 or 30 if you run e.g. bittorrent on a desktop.) http://www.sabi.co.uk/blog/ has some good comments about Linux's VM, and GNU/Linux desktops, being written by well-funded devs with their big fancy machines, and how GNU/Linux has serious weaknesses on memory-constrained systems. If you have plenty of RAM (relative to what you're doing), you don't have to care about lots of VM behaviour.
Another aspect of Linux that I remember figuring out was when I wanted to run cycle-accurate benchmarks of a routine I was optimizing. (http://gmplib.org/list-archives/gmp-...ch/000789.html) I ran my benchmark loop at realtime priority, so it would have 100% of a CPU core. When Linux scheduled it on the same CPU that handled keyboard interrupts, it froze the system until it was done. I found out that Linux (on my system, check your own /proc/interrupts) handles all interrupts on CPU0, and you can give a process all of a CPU without breaking your system by using taskset 2 chrt, to put it on the other CPU core. So for this I had to think only about how Linux's scheduler and interrupt handling worked (on amd64 core2duo). I didn't have to think about the network stack, the VM, the VFS, or much else.
Another time I was curious how Linux decides whether to send a TCP ACK by itself, or let a data packet ACK receipt of packets coming the other way on a TCP stream with data flowing in both directions. I never dug in enough to find out why it decides to sometimes send empty ACK packets, but not always. This behaviour isn't (AFAIK) connected to the scheduler, VM, or much outside the network stack.
So a lot of the things that are coming to mind that I've wanted to know about Linux have been possible to understand in isolation. Which sounds to me like your "multiple theories". But if by situation you mean workload and machine type, not what part of the kernel you're trying to understand, then I think I tend to understand things in enough detail that those things would be parameters in my mental model, so it's really the same model over all conditions for whatever part of the kernel I'm trying to grok.
I operate by delving into the details. I love details. (and, since I have ADHD, I have a hard time not getting wrapped up in details, as everyone can probably tell from my posts!) At the level of detail I like to understand, a complete theory of how Linux behaves on a whole range of hardware would be more than I could keep in my head.
This is maybe why I never saw eye to eye with on your wish for a complete theory that you could just remember that would tell you everything about how Linux worked. I didn't really say anything before, because I couldn't think of a polite way to say that didn't make any sense to me.