As written, a player can at most lose 2 HP on a “Disaster” result of a skill die roll. They can lose more if using the “Fickle Rolling” table (AKA using magic) and if the GM determines that the spell is powerful enough to incur an HP loss of more than 2.
The HP loss is irrespective of what the players are up against. This means the GM should only include injury as a risk for a skill die roll if it is reasonable for a player to lose 2 HP from that action. For example a player rolling a skill die for picking a lock doesn’t risk injury because the keyhole/door can’t feasibly cause the player to lose 2 HP, unless the door is trapped! If it is trapped, you would want to include that possibility when telling your player the risks involved in the roll.
Despite all that I’ve said, the game rules are meant to be bent and shaped how you want. If you and your players agree that big, boss monsters should cause players to lose more HP, then go for it!
As for HP increases, the idea is for those who do not take the HP increase on level up will become more likely to succeed at a skill over those who do take the HP increase. It’s a trade off between durability and success chance. In practice I am not sure if this trade off works well or not! I still need to do more playtesting (me and my friends trying out the game).