payer auth verifier causes session timeout error

[mc12345678]

but why would normal paypal express checkout payments also have the same issue?

When you say same issue, do you mean that the same mydebug log content is provided when only one user is going through checkout and that user is using paypal express (potentially with the other paypal module disabled)?

Otherwise, and also without searching through all of the code, there is the possibility that in this configuration that even using PayPal Express, a 3d secure "customer" may be directed through this same set of code that is attempting to change the session id after the session has been started without first closing the existing session and starting this new session.