Fix misuse of SYSTEM include flag to suppress warnings only for third-party headers

- Previously, SYSTEM was incorrectly applied to normal includes as well
- Adjusted CMake to restrict SYSTEM usage to external dependencies (e.g., FlatBuffers)

Signed-off-by: Yuvaraj Venkatesh <yuvaraj.venkatesh@arm.com>
Change-Id: If484b7fb8a708d571b47fb1f17c456d3e6e9849f