Can't you set it up to fake it though? Let's say you're in a room with 2 exits but one is hidden. If you're talking to an NPC about the room and in the dialogue ask about the hidden exit it will show up and then you can have markers to lead you that way. So, you can have an alternate path from A to B but A and B still remains the objective of the quest.
If you are REALLY creative... you could do things like set up an objective of "Kill Mini Boss - Demon" (or whatever, just for example), then have 5 routes... the GF leads directly through it, the GWF leads to a room with prisoners that will join you if you free them (give the GWF allies for the mini boss fight), the TR leads to a room nearby with a 'trigger' for a supposed trap system in that room (and just set the trigger to kill the boss), CW finds a vantage point where they can kill it/make the terrain around it kill it, DC finds a banishing ritual or something...
There are ways to kill an enemy without actually fighting it, so the path you are going down need not actually include the enemy lol, just a story line reasoning of how you defeated them without actually fighting them.
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Oh, more? Ok...
Imagine five doors, each with a skill required to open it. Five corridors leading to the same room, where the objective is.
That's the gist of it, and there are many many ways you can do this.
You can't have optional ACTUAL objectives/missions, however.
Wicks and Things: NW-DI4FMZRR4 : The Fenwick merchant family has lost a caravan! Can you help?
Beggar's Hollow: NW-DR6YG4J2L : Someone, or something, has stolen away many of the Fenwicks' children! Can you find out what happened to them?
Into the Fen Wood: NW-DL89DRG7B : Enter the heart of the forest. Can you discover the secret of the Fen Wood?
The Cursed Emerald:
There are ways to kill an enemy without actually fighting it, so the path you are going down need not actually include the enemy lol, just a story line reasoning of how you defeated them without actually fighting them.