It indeed solves the problem, thanks.
That said, the -Wnon-virtual-dtor option was set for g++ Debug only (not in the global project options) and "Append target options to project options" still tried to add it even though I was trying to compile with MSVC in debug, which means that "Append target options to project options" picked the project options, the MSVC debug options (as expected) but also the g++ debug options, for some reason. That feels like a bug.
On a side note, wouldn't it make more sense to put the compiler selection more important than the target selection? I may be missing some valid arguments, but I find it strange to have, for example, a g++ project, an MSVC debug and a g++ Release. I would expect that changing the compiler for one target changes it for all the targets and also for the project. From a UI point of view, it would mean putting the compiler selection box above everything else in the dialog.
Anyway, thanks for the pointers.
Note: don't hesitate if you think that the compiler framework redesign forum is a better place for the suggestion.
EDIT: actualy, even with "Use target options only" it sometimes adds the g++ debug flags to the MSVC command line. I don't understand anymore.