I think many people might agree with you that there are inefficiencies, however I don't think people living here would prioritize helping people getting visas over something else the MOJ could be spending time on.
The reciprocal tourist visa is working as intended for those countries in the agreement, and if you still need a visa to do something else e.g. study or work, that you better want to be here and thus be willing to put up with the minor annoyance of getting a visa.
EDIT: As far as companies and business travelers are concerned, you are probably already used to this, and so if you need to go on a business trip it's expected that you're prepared or you use a service to expedite your visa.
I live and work in the USA on a foreign passport. I tried applying for a Japan visitor visa at the Houston consulate. I was told that if I go back to my country of origin and apply there, I will be approved on the spot. However, this being a consulate in a third country, they claim they cannot accurately assess all my documents as their processing is "manual" and the experts for my situation are in their embassy across the Pacific!
I can't give the specific details, but they were nitpicking as to why they can't issue me a visa. Others in my company who have never even traveled here got a Japan visa back home, and multiple entry at that!
