Are all encryption tools made equal?
No, not all encryption tools are made equal.

Even when using the same cryptosystem, say AES-256, a tool's choice of cipher mode, how to generate AAD if present, how to generate IV, how to generate key, and the quality of the random source all affect quality.  The quality of cryptography engineering is the major deciding factor at that point and it is tricky to get right.

To determine if you should use VeraCrypt or let Comodo Backup do the encryption you need to assess the effectiveness of their cryptography engineering.

The simplicity of using the built-in encryption supplied by Comodo Backup is a significant convenience advantage.  If their crypto eng is up to scratch I'd make that your choice.