I disabled a couple of items using jv16 Startup Manager. Those items then completely disappeared from the list shown by Sysinternals Autoruns (a semi-official startup manager). By completely disappeared, I mean they were not even shown as present but disabled. The reverse was also true: I re-enabled the items in jv16 then disabled them in Sysinternals Autoruns, after which they completely disappeared from jv16's list.
I conclude from this that each startup manager disables items in its own incompatible way, and that only a single startup manager should be used. Is that correct? If so, I'd highly recommend including a statement to that effect in the jv16 Handbook.