GCC 5.4.0 is what came installed by default on my Ubuntu 16.04 desktop. I might change to a different compiler except that would be a lot of work, since I would then need to rerun hundreds of historical benchmarks, and it is not clear what would we learn by using a different compiler or compiler version.
We use many different compilers and compiler versions for correctness testing - various versions of GCC, LLVM, and MSVC with various optimization settings. That's important because different compilers generate different code and we want to ensure that they all generate correct code. (SQLite has found bugs in historical versions of all of those compilers!) But for benchmarking, as long as the same compiler and version is used consistently, does it really matter which compiler is used?
Additional compiler comparison data (from 2017): https://www.sqlite.org/footprint.html