Well, I just completed 「ラタトスクの騎士」 with Jacky’s help a little while ago. I was playing it on normal so I’m probably going to be replaying it on hard in the near future. Yes, there are two separate endings. After the final boss battle, there’ll be another fight with Emil against two other persons. Defeating them will net you the bad ending and conversely, losing the battle will net you the good ending.
Oh, and if anyone’s trying to figure out how to activate them 秘奥義s, you need to equip your character with the “スペシャル” skill, and then hold down on the B button after activating a advanced/high level tech attack. In Emil’s case, you can activate his after using 秋沙雨. It may work for other tech attacks, but I’ve only tried that one. I usually hit the B button again and then hold it down after using the B button to activate the “original” tech attack. It supposedly works with one just holding down the B button the whole way through but I haven’t tried.
And in case you’re wondering how long it took me, my total play time was about 33 hours. This would probably be a lot shorter if I figured out how to activate 秘奥義s before the final battle, but anyway…