The CPU tracer maintains a context stack based on stack operations that occur and uses that to deduce the deferred VBI. To be specific, a deferred VBI is deduced when the I flag is cleared in an immediate VBI context. I suspect the reason for the false positive is the stack switching your multitasking kernel is doing. I'd have to take a look at whether the logic can be tweaked; this logic originally came from the existing profiler, which is constrained to produce a properly nested scope tree, but this might not have to.
The shaded area is indeed the vertical blank period. The frame boundary lines within the shaded areas correspond to Y=0.
Manual markers are possible but first I need to get the detailed CPU execution trace integrated. Capturing the trace is already done, but the hard part is factoring out the tree view code in the history pane. That code is really complex due to the call and loop detection and also because it's integrated into a custom tree view control, which was needed because the standard tree view control in the OS keeled over and died on 150K tree nodes.