Am guessing they could probably strip a ton of fat out of the program by getting rid of skins and just calling the standard APIs.
It is nowhere near as simple. I don't work for JRiver, and I'm going on memory and extrapolation from what Matt has explained previously, but... It is something like this:
The Mac version of MC runs essentially (at the core) the exact same code as the Windows version. MC itself (the Windows version too) is built on a cross-platform framework that JRiver built in-house, which is why the Mac version exists at all. Unlike other cross-platform applications you've used, it isn't built on an "interpreting language" (Java or whatever). Nor are there two separately-developed applications which have to be maintained separately. There is the "core" (the vast majority of MC's code) and then the "OS-specific layer" which isolates what is absolutely required to work with a particular platform (so, the CoreAudio stuff on OSX, and the Direct3D stuff on Windows). It
is all "native" (it is all written in C++ and Objective C). But, unlike other "written for cocoa" applications, it wasn't all hand-written to use the OSX APIs. It uses, essentially, the "JRiver APIs" (which are then translated into native API calls where needed).
That's why the menus are hard, for example. They have to re-build a OS-specific extension to their framework so that the menus are themed right on OSX versus Windows (versus Linux). As it is now, it is using the same exact code Windows uses to build them (which is easiest, because it requires no duplication of effort to make sure changes are replicated across platform versions). So, said another way: It doesn't use the Windows APIs
OR the OSX APIs to draw those menus. It uses the JRiver API to draw them "raw" onto the screen. So, they need to build an OSX-specific version of that piece which draws native menus (or does a better job faking it).
I don't think this is that "hard" of a task, but it is probably a "big" task. There's always so much to do...
Hopefully this explains. But, it boils down to this: The way the Mac version of MC is built is unlike any other cross platform application you've probably ever used. It is actually a technological wonder, to a degree. So, they're not "going out of their way" to not use the Cocoa APIs. They aren't using ANY native APIs (on Windows or OSX) wherever possible, which is what allows a tiny shop to port a massive and complex application like MC across to different platforms, and keep them always pretty much in sync.