Do the campaign modifiers, such as regenerating health or invincible enemies, affect your score? It seems strange to include modifiers in the canned campaigns if they don't. I get why they would exist in a sandbox environment, but not here.
They don't, no. The trick is that you have to use every modifier by the end of the campaign; part of scoring 9/9 on the campaigns is knowing when to use what modifier where.
I imagine they exist because the campaigns are made up of the individual scenarios, and stringing three together doesn't really make the campaign feel much different.