By design, Cloudflare's WAF must MITM the connection between the client and your server, in order to perform its function. See Cloudflare's free SSL options require trusting them; what could they do to change that? and CDN end to end encryption? for more information.
To do this, Cloudflare must create a certificate for your site, keyed to a different private key than the one you created, which they store in their HSM. So, it would be expected that they public key in the certificate created by Cloudflare would not match the public key that corresponds with the private key that you created.
Notwithstanding, instead of using an online tool that requires you to upload your private key, you can verify that your private key corresponds with public key in your CSR and your certificate locally, using openssl.
As an example, I started with the commands that you posted in your question, to create an ECC private key, and a CSR:
openssl ecparam -out ECC.key -name prime256v1 -genkey -noout
openssl req -new -key ECC.key -out ECC.csr -sha256 -subj "/C=VN/O=Custom Organization/OU=Custom Organizational Unit/CN=*.domain.tld"
Then, you can use the command below, to show the public key that corresponds with the private key in the ECC.key file:
openssl ec -in ECC.key -pubout
This produces:
-----BEGIN PUBLIC KEY-----
MFkwEwYHKoZIzj0CAQYIKoZIzj0DAQcDQgAEKd3Wf7he+AReKhU45r+Bp/p8VeBQ
VCLsCPVkWMQc7jjMytJE0DWCY/FcJ+DepdUE7dSGmHIqu2VnmlO0uDJzGA==
-----END PUBLIC KEY-----
The command below can be used to extract the public key from the ECC.csr file:
openssl req -in ECC.csr -noout -pubkey
This produces:
-----BEGIN PUBLIC KEY-----
MFkwEwYHKoZIzj0CAQYIKoZIzj0DAQcDQgAEKd3Wf7he+AReKhU45r+Bp/p8VeBQ
VCLsCPVkWMQc7jjMytJE0DWCY/FcJ+DepdUE7dSGmHIqu2VnmlO0uDJzGA==
-----END PUBLIC KEY-----
As you can see, the public key extracted from ECC.csr matches the public key derived from ECC.key.
The following command can be used to extract the public key from a certificate file:
openssl x509 -pubkey -noout -in cert.pem