How does the owner of the DNSCrypt server know that you are using Tor? You are just another regular user. You can also hide your IP from the DNSCrypt server by using anonymised DNSCrypt relays, ODoH, or DNSCrypt over Tor.
On the other hand, if you use Tor DNS, you are actually using the DNS of the Tor exit node. So the exit node will see your encrypted traffic if you’re using https, which it can’t modify. And unencrypted DNS, which can be spoofed. All your data is in one place. So using that data, a malicious exit node could potentially perform a MITM SSL Strip attack. Whereas DNSCrypt prevents this from happening. You may have heard the old story of cryptocurrency being stolen by malicious Tor nodes a few years ago.