Well, that's magic then, because it cannot work.
For --prefix= to work, you need to call wxStandardPathsBase::SetInstallPrefix(), which I forgot to add in 3194.
Plugins and resources are found (or not found) using wxStandardPathsBase::Get().GetDataDir() since 3194. This has not changed in 3245, and the changes in 3245 are more or less unrelated to the actual plugin/resource paths (short of a ?: that sets user = global in "relocated" mode).
My much-discussed /proc/self code affects GetAppPath(), but not the other ones.
wxStandardPathsBase::Get().GetDataDir() returns a global variable that you can set using above function (which we aren't doing), and which it fills it when empty. For that, it appends the application's name to wxStandardPathsBase::Get().GetPrefix().
That latter function, yes you guessed it, uses readlink("/proc/self/exe") to get the application's location, removes everything after the last "/bin/", and finally hardcodes /usr/local/ as a fallback in case anything goes wrong.