It's always bad when the UI offers two ways to do the same thing without really explaining what's the difference. It's equally bad when UI uses some meaningless techno jargon such as "cairo" :) Unfortunately 0.46 was released still in the middle of a transition period which made both these evils inevitable. Now that we're in 0.47, however, I would like to address this issue by switching all of PS, EPS, and PDF output to cairo, removing the builtin Inkscape exporter, and purging the mentions of "cairo" from the UI.
As a matter of fact, this has already partially happened (not sure who did this). Right now both PS export options work via cairo and produce identical output. The Inkscape-native PDF export is nowhere to be seen. The only exporter which still uses native code is EPS. However, since 1.5.2 cairo can produce EPS files too, so this can all be done in one place now (closng several EPS export bugs along the way). The only downside is that it will require cairo >= 1.5.2, is everyone OK with that?
By the way, the latest cairo 1.5.12 finally fixes the bug where zooming in too closely in Outline mode produced messy broken lines. Now everything is neat and clean. Upgrade is recommended.