The XML Signature secure validation mode is all or nothing, there is no way to selectively control each of the restrictions. The mode is enabled either by setting the property "org.jcp.xml.dsig.secureValidation" to true with the javax.xml.crypto.XMLCryptoContext.setProperty() method, or by running the code with a SecurityManager.
It would be useful to define a new security property that allows you to configure the individual restrictions that are enabled. For example:
jdk.xmldsig.secureValidation=xslt, md5, refs > 29, \
trans > 4, uniqueIds, uri = file | http, \
retMethodLoop, DSA keySize < 1024, \
RSA keySize < 1024
An administrator could selectively control each restriction, and could remove/disable a single restriction without having to completely turn off everything.