Generally, you will have a table of flags (usually booleans). When an event is completed you will set the flag for that event as true, or completed.

In your case, let the player access areas A and B; when they kill boss Z set flag BOSS_Z_KILLED to true. When the player tries to enter area C, check to make sure that BOSS_Z_KILLED is set; if not, deny passage, else, let him continue.

The increased difficulty route is an option, but you'll need a flag table in pretty much any RPG. Besides, more difficult areas can be exploited by the player if the game isn't balanced well. What if player manages to kill a beast many levels higher than him and he levels up 20 times?

If you absolutely don't want the player to go somewhere, you need to make it impossible. This means using either clip regions (i.e. the classic "fat-NPC-guarding-a-doorway" trick), dealing a bazillion damage to the player if they try to pass so they die every time they try, or some other technique that you've probably seen in plenty of games. Making a section "too hard" for a player might work, but it's not a guaranteed approach to limiting player access.

Most of the time there's just a locked door. If there's a scripted event you're being forced to follow, there might be a party member that pulls you up whenever you try to go the wrong way. But still, most RPGs just lock the door.
The Zelda games control progression using upgrades. Every item you collect needs to be used somehow to open up a new area. The Metroid games do this too.

Consider firstly whether it's absolutely critical that the area be locked off. If progression is a measure of player ability scaling (levelling, new weapons, new armor) then it's relatively trivial to create a difficulty barrier, in which case... do you absolutely need to prevent the player from getting to Boss Z until a series of conditions are met?

Part of the fun of explorative/non-linear RPGs (which yours may be, I'm not sure) is giving the player the autonomy to 'break the rules' so to speak. In Fallout 3 for example, I know I can go to almost any part of that map from the moment I leave the Vault. The first time I played, I ran off and got insta-gibbed by a Deathclaw. That was a really fun and exciting moment, because it really clarified the world as a dangerous place.

If, however, it is important to put absolute roadblocks in the game, then camouflage your intent as much as possible. To use Fallout 3 as an example again, something it does not so well is the inclusion of the occasional safe/computer terminal/door that cannot be bypassed but requires a key. It feels contrived, and could have been easily masked with new models/textures to give the impression that we're encountering a new, special obstacle.

And obfuscate the game logic with story logic. Don't simply throw an invisible barrier or insta-death zone into the game - ensure it's logically consistent within the narrative. The GTA series has made a bit of a motif out of 'under construction' bridges to prevent access to new areas of the city until the narrative has progressed to a specific point. It can feel contrived, but it fits within the universe of the game, does its job, and isn't so blatantly anti-suspension of disbelief as a "You cannot go this way at this time" message popping up on the screen.