I am not aware of an existing mechanism to detect the .ph files and build them. A simple way could be to add something like this in then Makefile.PL:

if (!eval { require "sys/syscall.ph"; 1 }) {
    my $save_pwd = cwd;
    chdir "/usr/include" or die $!;
    system("h2ph", "sys/syscall.ph");
    chdir $save_pwd or die $!;
}
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Of course, this should be only run on Unix systems. But not all Unix systems have include files installed, so one has to be protected from this fact. Also, Makefile.PL is often not run under root permissions, so the above would fail. It's also possible that even "make install" is not run as root, so maybe it should also be possible to install the .ph into some other directory.

Or maybe it would be safer to not use .ph files at all and move the required stuff into an XS module?