I already did that in an earlier post. You just need to have 0 bonus at the end of a level. So you can not skip it in every level, as there are some gems that you cannot avoid and dying on purpose to reset the bonus will also remove all your power ups, which will probably slow you down much more than what you would gain from the bonus skip.

I'm not a moderator for this game, so I can not say anything about the rules and the emulator setup for this game. We are just discussing the problems with the timing for now. Removing the bonus countdown from the timing will also make all the setup for it during the levels obsolete.

The game itself most likely will use fixed addresses in Chip RAM anyway, so adding Fast RAM won't matter. But WHDLoad needs Fast RAM to preload the disk images, which is usually what you want to do. Without preloading WHDLoad has to reenable the OS and load data from the harddisk, which will then depend on the disk speed again.