Has it actually been verified that the glitch updates both counters?
No, but you could try it out by using glitches

There might be a set total of morality points you can get from each area in the game and the game calculates from that (which would allow cheating by glitches), but I think it's far easier to program it with both sides of the ratio being calculated every time an option for morality points occurs. This has the added bonus of preventing cheating by using glitches (though of course during development you try to realize making your game glitch free

)
I have no hard proof it actually works like this though.
Again, why?
Because it 'forces' the player to have a Shepard from ME1 to have the most options. (between parentheses because of master race

)
A fresh ME2 character can go full paragon to pass all paragon checks, full renegade for all renegade.
A full paragon ME1 character can go either way, it has to go full renegade to pass all renegade checks though. Renegade vice versa.
A mixed morality ME1 character can go either way.
You don't even have to have full bars in ME1 to achieve this. It's not like it's hard and forces you to grind to ME1 all the way everytime.
Maybe it's not how it should be, but I like it a lot.