I would be a little bit careful first about whether that is real staining. The green channel (if that is what it really is) is notorious for autofluorescence from red blood cells, lipofuscin, etc. In general, I would expect the FoxP3 to either overlap with the DAPI staining or be cytoplasmic, and in your case I am not sure if it is either. Do you have a negative (secondary only, no primary) control to verify that your staining is really FoxP3?
The problem with combining the channels would likely be balancing the intensities from unrelated channels. If the staining is exclusive (and it looks like it is not always since some objects are picked up in both samples) enough, it might be better to run StarDist twice and keep both sets of results, then delete results from one that are inside cells of the second run. I would definitely verify the staining first though.