The trooper's statements do seem to indicate infamiliarity with the MPA.
However, I share the opinion of some that you don't get to pick MPA or CHL, whichever is more convenient. It is my opinion that when your CHL is issued, MPA goes out the window, even if the firearm is being transported in a manner allowed by MPA. Say you typically carry one in the console, but one day you have left your CHL on the dresser. If you get stopped, don't expect to convince the officer that you were carrying under the MPA, so your license wasn't required.
The OP's situation would best be addressed by more information displayed in response to queries, such as 'Approved-pending receipt', 'Mailed to recipient on 00/00/0000', or something to convey it may not yet be in possession. This would not require legislation, as it is just procedure.
This warrants a discussion with the DPS department head that has corrected other processing issues.