I think that this is the kind of thing that you can answer yourself with a bit of experimentation.
More in general, it is useful to remember that it is possible to combine different types of stops but in that case we should keep in mind their order precedence.
Thanks for replying. I have verified my own question. The answer is yes. I tried to post this several hours ago but the post was awaiting approval. The original post is still awaiting approval. Not sure why.
I don't know how did you arrive to your incorrect conclusion, but the answer is that multiple ApplyStops are of course supported but they have to use different TYPE.
If you use two or more ApplyStop with same type (stopTypeLoss) the LAST call to ApplyStop will overwrite anything that was set earlier for that particular stop type. That way you OVERWRITE stops defined in the Analysis Settings. Anything in the code OVERWRITES stops defined in Analysis settings.
The reason I delete is because I'm afraid it will mislead other readers. Some people don't read the entire thread. Anyway, I have restored the post as I respect your wishes.