[@Sven the Silent]
Mainly because it gives players choice and diversity.

For the Super Mutants, First and foremost its set well over 150 years since the Master and the creation of his super mutant army. Which gives them enough time to spread out. If we go 'It wasn't mentioned' with all fan-based roleplays, they will all eventually dry up and become clones of each other. Creative Licence aids roleplays. 

As to Synths, not all Synths are loyal to the Institute, look at the Railroad. So may have gone to Canada to flee from them. Also remember that there are Synths that don't even know they are Synths, take Harkness for example.

This Roleplay is set in 2290, 2 years after the main quest line of FO4, and if you notice, with the Brotherhood at least, Transport is becoming a lot more flexible.

Also you have to remember that Vancouver is a costal city, which could 'easily' be traveled to by those with access to boats or ships.