To solve it;

1. as @Tilman Hausherr mentioned, one should add required dependencies

https://pdfbox.apache.org/3.0/dependencies.html

2. as @Tilman Hausherr mentioned, one should add the provider as below

Security.addProvider(new BouncyCastleProvider());

3. as @mkl mentioned, one should change the signatureAlgorithm on
   

https://github.com/apache/pdfbox/blob/3.0/examples/src/main/java/org/apache/pdfbox/examples/signature/CreateSignatureBase.java

ContentSigner sha1Signer = new JcaContentSignerBuilder(XXX).build(privateKey);

where (in my case) for domain certificates, XXX= "SHA256WithECDSA"

PS, one can find the working project at https://github.com/tugalsan/com.tugalsan.blg.pdf.pdfbox3.sign/tree/main