I had a similar problem with my real tube amp. Boosting in front of the amp didn't result in increased volume - just more gain. I solved this by using my boost (Xotic RC Booster) in the FX loop, effectively placing it between the pre amp and power amp (correct me if I'm wrong here).
This pedal is very transparent anyway, but I set it with increased volume and minimal gain to maintain the tone. I could get huge increases in volume this way, so it worked perfectly. I've sold my amp and am now going to be using an Axe FX II only setup, so this is something I'll be looking to address.
There are so many options, but ideally, I'll find something I can use like the above real world example. Then I can just incorporate it into a scene.
Hellbat - you mentioned "a clean boost available at the output as well" - can you please elaborate on this? Is this something that isn't available when not using scenes? Or do you mean that scenes give you the ability to configure different output volumes?