Will there be a new speedrun category for the version, or will rules e.g. the rule to set the settings to default, change to set it on default and turn boss checkpoints off?

no there wont be any changes to the rules due to the new version having an extremely slim time save and default setting keep it off

So boss checkpoints are allowed?

ok so I guess they are turned on by default so yea boss checkpoints are allowed. (Thought they were turned off by default)