It really doesn't. Unless the ECU is mapped for it, then you can put in whatever you want and it won't make the blindest bit of difference.
Of course, you can run more boost or advance the timing if you're running 105 for example, but again that just reinforces the point that it's all about the mapping. Standard, FI or engine swap, you won't see the difference unless mapped.
If you have to run 99 because you get substantial knock on 97, then I'd be having a strong word with the tuner personally, For example, my MR2 runs as happily on 97 as it does on 99, and I notice more difference in the power when the temp drops than I do on any fuel I put in.