I would shoot for a proper action and let the truss rods do what they do to get it there.
I was flummoxed at first by TWO truss rods. Your head says they should be equally under the same tension. Ain't necessarily so . . . .
These are laminated necks. I would be VERY surprised is the wood on the high side were exactly the same as the low side, even with ALEMBIC's serious commitment to using properly-aged / dried woods. Plus it acted one way when brand new, differently now. And will act differently in the future, possibly. This would make me think maybe it's not exactly the same torque values on the truss nuts. They are VERY stiff necks, with the 1/4 ebony and who knows what laminates, but they do move, some more than others. I now think that the truss rod tension should maybe be in the same neighborhood, but I no longer think equal is a rational target.
And we always notice this with a new (or new to us) guitar, until we get it like we want it. This bass is now in a different environment, probably with different strings with its new owner, and it was way out when you got it . . . so what you've described is not unexpected.
Barring hearing awful creaks and moans from a way too tight truss rod, I would let them do their job.
If you are using the feeler guages (or you could use other things to measure this if not), I will check the relief on both sides, under the G and then under the E or B. If they are the same or very close, then you're there with most necks. A few may show a noticeable difference, but if it plays right, you're there. Every neck is different and they don't all adjust the same, it's just down to the vagaries of wood. Don't be surprised if you keep chasing your 'right' set-up for a few more months as the bass adapts to your work. The good new is older basses typically move to a new set-up and generally stay at those values once it takes a 'set' finally.
As always, my method is for reasonable necks in good condition. Obvious big problems, as always, need to be evaluated by a professional repair person.
Here's two links that are very helpful:
http://www.garywillis.com/pages/bass/bassmanual/setupmanual.html and . . .
http://www.jerzydrozdbasses.com/akcndfr54jdhrei567/Ultimate_Guide_ver100.pdf There is a very subtle yet noticeable interplay between string tension, neck relief, bridge/nut/ string heights that govern setup. There are no empirical measurements that work for everyone. You sound like you've done it by the book in a methodical fashion, and the bass has responded properly. Well done.
J o e y