The post 04 bikes only have bypass screws and no trim pots.
The way it works is the axone can set an engine variant 1 or 2 with 2 being open loop (no cats in exhaust).
The 2 variants use the same map but interpret the bikes sensors in different ways (ie: lamda ignored in variant 2).
That map can be updated as Aprilia bring out updates or there is a special map you can load if you have the Aprilia evo 6 system.
It gets referred to as switching maps between 1 and 2 but provided your map is up to date no switching happens when going from closed to open loop just a software switch toggled.
With the setting of the Tb's you don't need an axone generally just a gas analyser. An Axone is handy to check the vac readings which should have a 30 mbar stagger when the co is matched. Provided your confident you have no vac leaks you can do without it.
The only exception is if the bypass screws cannot balance the tb's with their range which i would only think would be down to a fault or some heavy mods etc in which case if you have the password (and most dealers don't, Griff does) you can alter the co electronically via the axone.
Tb's should always be re synced after the variant is switched or a new map loaded.
Between 06 - 09 rsv's Aprilia introduced no map updates the oem is still current.
Hope that makes it clearer.