I thought the point of Fil-C was to be a drop in safe replacement of C. This project existing implies it isn't. What's going on?
It isn't entirely drop-in for all programs.
Most large C code bases aren’t really written in C. They’re written in an almost-C that includes certain extensions and undefined behavior. In this case, it uses inline assembly (an extension) and manipulating pointers as integers (undefined behavior).
QtBase is C++ first of all.
Massive projects like Qt also push compilers to their limits and use various compiler-specific and platform-specific techniques which might appear as bugs to Fil-C.
Afaict, there are some patterns that are not supported, like converting pointers to/from integers and doing stuff with them like bitmasks (which is a huge anti-pattern, but some code bases do it)