Are bosses considered enemies?
Yes
Bosses are enemies and have their own level.
Does Gutterdie's after effect adds an enemy if you are in the endgame?
Yes
The Gutterdie's after effect that adds an enemy to the next engagement if you suffered damage, is intended to apply even during the endgame.
About enemy Drone Alone 3: Can I change any two misses of the same colot to two crit hits?
No
The reward on Drone Alone 3 allows you to change two misses of the same color, both into basic hits for a total of 2 hits.
Are basic and crits both considered hits?