Unfortunately, compatible axioms don't guarantee compatible code on top. The big problem is the operations that use "system" (e.g. date and ensure-dir) break on different OS's. This is the root of many of the Windows problems.
For this reason, I believe that use of "system" makes a mockery of the axiomatic construction, and has no place in the Arc core.
But at the very least, if both standard Arc and offshoot implementations both use system, they'll both break in the same way. Therefore code will still be "compatible" across Arc implementations (in that it will generate the same error messages on all implementations).
Yeah, I know that doesn't fix the problems you mentioned, and yes, I run Windows so I do encounter those problems with the vanilla Arc releases. But we can't expect a offshoot implementation to do anything about the problem, we really need pg to solve the problem at the source.
While Unix did win, that doesn't mean that Unix's names won. It's Unix's features that won. So it's reasonable to provide certain operations, but implementing them in terms of (system "unix-command-name ...") is not.
Of course, I use Mac OS X, so it's not like I'm adversely impacted. But the point still stands.