Isn't the simpler conclusion here that one should look for the signature where it is supposed to be? Instead of using an excessively general XPath like "//ds:Signature" that might find any signature in any unexpected location...
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If you are an IT admin with any pride, SAML is out of any future plans. The idea of SSO is suspect as a whole. Xml parsing has been hit twice in a week, avoid it in the future, anything wrong with a policy that replaces xml with json?
Obviously, if you can avoid doing SSO with SAML, you should.