99% of the time they are of no use once a layout is released. The settings (apart from possible stake, prize and percentage) combinations are of little use. Things like less flashy attract mode for venues that don't want the machine to be too distracting, odd percentage (so adding 1% to percentage payout), and stuff like that. On some machines it'll switch between different profiles (softer for pub, harder for arcade), again the options are pretty much limitless.
By all means tinker, you can't really break a machine (worst comes to worse you can re-extract the layout). Best to make changes with the machine's virtual doors open, then closing the doors should reboot with new settings.