I got the message "Unable to revert mtime: /usr/local/share/fonts" (see also related bug 909728) upon opening a particular pdf file with xpdf and discovered this message was emitted after it had created a .uuid file in that directory (which was writable by me as normal user, probably something I did in the past), so clearly libfontconfig still writes to /usr under some circumstances. I'm using the latest fontconfig in sid (2.13.1-2+b1).
relevant strace output: access("/usr/local/share/fonts/.uuid", F_OK) = -1 ENOENT (No such file or directory) stat("/usr/local/share/fonts", {st_mode=S_IFDIR|0775, st_size=4096, ...}) = 0 openat(AT_FDCWD, "/usr/local/share/fonts/.uuid.TMP-gyDVw4", O_RDWR|O_CREAT|O_EXCL|O_CLOEXEC, 0600) = 5 link("/usr/local/share/fonts/.uuid.TMP-gyDVw4", "/usr/local/share/fonts/.uuid.LCK") = 0 unlink("/usr/local/share/fonts/.uuid.TMP-gyDVw4") = 0 unlink("/usr/local/share/fonts/.uuid.NEW") = -1 ENOENT (No such file or directory) openat(AT_FDCWD, "/usr/local/share/fonts/.uuid.NEW", O_RDWR|O_CREAT|O_CLOEXEC, 0644) = 5 rename("/usr/local/share/fonts/.uuid.NEW", "/usr/local/share/fonts/.uuid") = 0 unlink("/usr/local/share/fonts/.uuid.LCK") = 0 utimes("/usr/local/share/fonts", [{tv_sec=1573279099, tv_usec=455382} /* 2019-11-09T06:58:19.455382+0100 */, {tv_sec=1573279221, tv_usec=252001} /* 2019-11-09T07:00:21.252001+0100 */]) = -1 EPERM (Operation not permitted)