The struct_stat64 declaration forces align(4) on st_size. This is wrong for ARM, I wonder if it's actually correct for x86? Should be trivial to fix, but std.file probably should define this struct at all. It should use core.sys.posix.sys.stat instead, which currently does not have a struct_stat64 definition. Filed here, so it won't be forgotten.
This should first be fixed in phobos - which should not be defining it's own version of struct statfs at all. It should instead use the druntime version. There is an open ticket somewhere in D.bugs - flag it again and raise a pull request to remove it entirely, and update any parts that may break as a result.
https://github.com/D-Programming-Language/phobos/pull/819 Got rid off all the old *64 functions. (struct_stat64 is actually deprecated). I still have to check whether druntime's stat_t is correct though.
I do believe this is fixed now.