Maybe the answer is to 1) add a parenthesized option REINDEX(SYSTEM) (to allow the current behavior); and 2) make REINDEX DATABASE an alias which implies "SYSTEM false"; 3) prohibit REINDEX (SYSTEM true) SYSTEM, or consider removing "REINDEX SYSTEM;".
That avoids the opaque and surprising behavior that "REINDEX DATABASE" skips system stuff but "REINDEX DATABASE foo" doesn't, while allowing the old behavior (disabled by default).
