For context, let's look at this:
The idea that there is no canon is a bit silly at times. It's not that we don't have any. It's that we have a multitude which touch, cross, and dip into each other.
This does not really refer to the Canons as a concept. It refers to the general site-held idea that "there is no canon". Usually, that is embodied by users' individual beliefs on which article on (or not on) the SCP Foundation Site would be deemed canon by said user. Sometimes, the canons various users believe in may overlap with another user's.
Can it be said that the canon storylines take place in branching timelines? Or like each canon storyline is a timeline within itself?
That really depends on the specific canon itself. For some (e.g. Unfounded), they represent a scenario that cannot co-exist with conventional Foundation-verse (since the Foundation does not exist here). Some (e.g. Doctors of the Church, Broken Masquerade) are hinged on radically different interpretations of the Foundation that do not necessarily fit in with conventional Foundation-verse. And then, some (On Mount Golgotha) do not have huge issues fitting in with conventional Foundation-verse.
