1) He is avoiding some sort of corrupt signals intelligence folks from knowing what he's working on.
2) He is avoiding the government catching him in some corruption by avoiding the official records act.
Anything else?
Or the same reason I have Whatsapp - communication in my social groups happens there, and if I don't have it I get left out.
Your explanations assume there is some deeper meaning, looking at the tradeoffs for each communication platform, and then coming to some rational conclusion. I don't think there's much evidence for that.
The people around trump just happen to be used to using signal to communicate, and if Pete doesn't get on board he gets left out.
We have to assume malicious intent. These people could start a nuclear war. They get zero flexibility or grace.