In my high score run, i have had a few waves where the next wave would spawn and i would micro a tower to mop up the previous wave. Still got the full clean bonus. I think as long as you clear a specfic wave before 30 seconds, you should be fine.
About killing boss frogs, actually killing one OSfrog wave instead of getting high frogs will net more points. I remember seeing the message 'Boss Wave 5 cleared' with an estimate of a 25k point bonus attached to it.
Not leaking the elemental is vital in scoring high (preserving clean streak). I remember i had to spam arrow towers to get rid of the final part of the lvl 3 Nature ele to not leak xD