You're correct and you can see it working with the dig command.
Before adding the entry
$ dig duckduckgo.com
...
;; ANSWER SECTION:
duckduckgo.com. 182 IN A 52.142.124.215
...
After adding the entry
$ dig duckduckgo.com
...
;; ANSWER SECTION:
duckduckgo.com. 0 IN CNAME safe.duckduckgo.com.
...
EDIT: I've not used the CNAME feature before in Pi-hole. I noticed the text regarding CNAME limitations. Sure enough, although the above enables the CNAME, it stopped the duckduckgo.com domain from working. To fix this I tried adding the safe.duckduckgo.com IP address to the local DNS, and that fixed it.
To summarise:
Local DNS > CNAME Records
Domain --> Target
duckduckgo.com --> safe.duckduckgo.com
Local DNS > DNS Records
Domain --> IP
safe.duckduckgo.com --> 52.142.126.100
$ dig duckduckgo.com
...
;; ANSWER SECTION:
duckduckgo.com. 0 IN CNAME safe.duckduckgo.com.
safe.duckduckgo.com. 0 IN A 52.142.126.100
...