After reading through all the evidence in the OP, I disagree with Conceptual Manipulation entirely.
The issue I have with Conceptual Manipulation here would be the fact we aren't given any direct or implicit quantifications for what "time" is being referenced as. What we're given is that after Dark Danny fuses with Clockwork, who embodies time, it causes time and reality itself to start glitching out and dissolving. This isn't enough evidence to assume "time" being referenced here is the conceptual idea of time itself rather than just the physical understanding of what time is. Time in itself isn't inherently an abstract concept without physical implications, time generally just denotes the "
continued sequences of existence and events" across reality. So until I see further evidence supporting an ontological interpretation rather than physical, I disagree with assuming this would be Conceptual Manipulation.