We are not sure 100% what you want to do.

1. Probably you want to emulate Acrobat's behavior when user clicks on 
signature area and signs document. In this case we should apply standard 
Acrobat signature approach.

PdfReader reader =new  PdfReader(src);
FileOutputStream os =new  FileOutputStream(dest);
PdfStamper stamper = PdfStamper.createSignature(reader, os, '\0',null,true);
// Creating the appearance
PdfSignatureAppearance appearance = stamper.getSignatureAppearance();
// linking PdfSignature with acroform signature filed (not necessary)
appearance.setVisibleSignature("SignatureField1");
appearance.setCertificationLevel(PdfSignatureAppearance.CERTIFIED_FORM_FILLING);
// Creating the signature
ExternalSignature pks =new  PrivateKeySignature(pk,"SHA-256","BC");
ExternalDigest digest =new  BouncyCastleDigest();
MakeSignature.signDetached(appearance, digest, pks, chain,null,null,null, 0, 
MakeSignature.CryptoStandard.CMS);

2. In case you want to sign a specific Dataset of an XFA form and you 
want the signature to be validated by Acrobat, you should use the 
XmlDSig approach, because Acrobat doesn't support XAdES (yet):

PdfReader reader =new  PdfReader(src);
FileOutputStream os =new  FileOutputStream(dest);
PdfStamper stamper = PdfStamper.createXmlSignature(reader, os);
XmlSignatureAppearance appearance = stamper.getXmlSignatureAppearance();
appearance.setXmlLocator(new  XfaXmlLocator(stamper));
appearance.setXpathConstructor(new  
XfaXpathConstructor(XfaXpathConstructor.XdpPackage.Datasets));
ExternalSignature signature =new  PrivateKeySignature(pk, digestAlgorithm,"BC");
//use signXmlDSig instead of signXades
MakeXmlSignature.signXmlDSig(appearance, signature, chain);


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