so will the ends when you beat him be dependant on how many bad endings you got? and also why doesn't the protagonist send out the clones to scout. leaving the original to drink lemonade in the ship
It's very likely that some of the final endings will be based on how many bad endings you got, at least partially.
The canonical reason that the protagonist doesn't send out the clones to scout is because the use of cloning technology is heavily frowned upon, and Vulpis can't handle more diplomatic incidents. To that end, your ship AI refuses to allow multiple able-bodied versions of you to be wandering around at once. There's even a bad-ending where this happens by mistake.