Both signal and molly are considered safe, a lot of apps use the same protocol as signal, most risk come from messages leaks before the encryprion happens.
Unfortunately, I'm not aware if they did external audits, but both codes are available in github.
There's a hardened "version" of signal called molly
Also because most phones have operational system's that are more secure than Windows, so a app is a easy way to block everybody that don't fit a profile of optimal users and avoid problems/hacking.
Companies dream of a closed internet accessible only from a controllable environment.
That's a big one, you can disable it, but if the other person has it enabled there is a possible leak after decryption also.