When the "Enable the editing toolbar" (i.e. the 2010 wikitext editor) setting is enabled in the "Editing" section of Special:Preferences, the Proofread Page-specific options Show header and footer fields when editing in the Page namespace and Horizontal layout when editing in the Page: namespace in the "Proofreading interface options" section are hidden.

Since these two options are literally exposed to the user as buttons in the editing toolbar (albeit with different button icons than in the preferences), hiding them when the toolbar is active seems rather counter-intuitive. Actual user confused about this reported the issue on enWS Scriptorium, and it took me quite a bit of fiddling around to figure out what's going on enough to write it up here.

The conditional hiding of these may be related somehow to global prefs (I don't recall seeing this issue prior to roughly that timeline), but that's just a guess.

From a UI perspective it would make sense to flip this behaviour: show the PRP options when the editor is enabled. Provided I've managed to twist my brane around why the current behaviour is as it is (iff it is intentional), perhaps the most sensible approach would be to never hide the options but add a label that explains why they may be overridden in practice (i.e. always showing them is less confusing than the alternative).

A more long-term fix is probably to obsolete these two preference settings in favour of UI and behaviour changes in PRP that make them unnecessary. Those who prefer the so-called "horizontal" setting know how to flip it, and if that is remembered it may no longer need to be a hard pref. And if the header/footer were visible even when collapsed (i.e. with a disclosure triangle, a small grayed out text label, or other UI affordances) and the user's run-time toggle remembered, then that pref too could probably go.