Apple's Mail Privacy Protection

Apple Mail Privacy Protection is a service provided by the Apple Mail app. Apples states it “works by hiding your IP address and loading remote content privately in the background, even when you dont open the message. This makes it harder for senders to follow your activity” . “Protect Mail Activity routes all remote content downloaded by mail through two separate relays operated by different entities. The first knows your IP address, but no the remote Mail content you receive. The second knows the remote Mail content you receive, but not your IP address, instead providing a generalized identity to the destination. This way, no single entity has the information to identify both you and the remote Mail content you receive…”

The helm server provides Spam and Security setting. Would enabling Apple’s Protect Mail Activity override the default setting for Helm’s Spam Assassin?

The Apple feature you are talking about it relative to tracking, not relative to spam.

Turning this on shouldn’t affect the effectiveness of Spam Assassin, unless there’s something I’m missing.

This is correct. By the time apple mail is able to view a message, it has been delivered, meaning it has already passed through any content filters (including spam assassin).