Generally, yes. The benchmarks are calculating/computing the same things on both architectures, and the various sub-benchmarks are based on real-world non-trivial computational problems rather than microbenchmarks that are easily manipulated by instruction set differences.
Unless they are written in optimised Asm I would not compare across architectures, because there is considerable leeway in compilers and my experience has shown that a good human can often beat a compiler solidly --- at least on x86.
If anything, I feel like many tests are based on x86 special instructions like AES, which does not directly translate to other tasks. But for most of the tasks I think it wouldn't be possible that the processor are only better at those and performance of most program should correlate with geekbench score.