This is not a deficiency in PTO.  It is just how the IRS' e-File Schemas work.

I agree it would be preferable to have the e-signatures as well as e-file acknowledgements attached to the return.  The IRS is still at the early stage of adopting anything electronic and does not accept electronic or digital signatures for various documents.  Part of it is from its concerns about the risk of taxpayers disavowing signatures provided in electronic forms.  So, this really involves both legal and technical issues that will take some time to resolve.

For now, the process is a bit fragmented.  But it doesn't mean that these separate documents are informal or not authoritative.

First of all, the metadata for e-signature is embedded in F.8879 even though it is not printable.  Similarly, the E-File Confirmation Letter (which is a substitute for F.9325) is attached to the return and can only be printed from the return that was e-filed.

As you are aware, the IRS is authorized by the statue under §6061(b) to "develop procedures for the acceptance of signatures in digital or other electronic form."  F.8879 and F.9325 are the products of these guidelines.  Pub 1345 clearly outlines the relevant rules and requirements for e-filing which, in turn, is governed by FTC rules, Government Paperwork Elimination Act (GPEA), Electronic Signatures in Global and National Commerce Act (E-SIGN), Uniform Electronic Transactions Act (UETA), and various NIST standards.  There have been some very careful deliberations on the IRS' part what constitutes acceptable signature, legally speaking, for tax purposes.  All of that makes this one hot bowl of soup with plenty of alphabets that could make a mess if it lands on someone's lap.

The existing process definitely has much room for improvement but, for the reasons stated, I would certainly stand by the use of those separate documents as official proof of filing.