I can't tell you the exact solution, but I had a quick look at your problem and I'll make some suggestions where you might want to look deeper.
IO::Socket::SSL uses Net::SSLeay as its wrapper around OpenSSL. The POD for the latter says it doesn't have a complete x509 interface and that dump_peer_certificate returns "selected" information.
There is a low-level routine in Net::SSLeay called sslcat that does more general things, including grabbing the whole certificate.
Perhaps using the lower-level Net::SSLeay stuff will get you a certificate you can save to a temp file and specify to Crypt::OpenSSL::X509. I haven't tried it, but that's where I'd start based on the docs for these three modules.
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