I'm not 100 percent positive, if I understand your problem, but I think it's possible with some R scripting. You have a list of (know) compounds and hence also their m/z value
and you want to retrieve the isotope intensities from all aligned samples. Is that so far correct?
The isotope detection assumes, as a general screening, unmodified/unlabled compounds, so this moderate performance is not surprising.
The next update for CAMERA includes a possibility to adjusted the allowed m/z differences and the intensity window, so molecules with heteroatoms like Cl should be recognized.
But as I mentioned above, a small script should solve your problem.