Hello everyone, to whom may be interested in how it ended up, here's a follow up.
I returned the Onkyo and opted for a Denon AVR-X3700H for it's pre-amp capacity.
I also added 3 cheap but no bad Fosi (2x160w on paper) mini amps and an Infinity aircom T10 cooling device since yes the Denon does get hot.
I was helped by Trepdp83 who gave me advices.
I could have used any combination to hook-up both Bose AM16 but I went with one for the surround and one for the heights and one LFE output for each. Since I did want to use all 12 speakers, I had to trick a bit so one Fosi bridgeable mini amp went for the surround back (had just one previously installed in my former surround set-up), I use both pre-outs to the amp wich feed a single back (helps in the settings afterwards to make the amp believe there are 2 speakers in the back!).
I've another Fosi to feed both rear heights (2 assignable, not amplified pre-outs) and finally the third one is hooked to another set of fronts speakers from the pre-outs in addition to the already amplified ones, so 4 speakers in the front.
I then have an actual 6.2.4 Atmos setup (amp thinks it's a 7.2.4) with 4fronts).
I liked the Bose sound before (sorry if I'm not a "true" audiophile but I do like this bassy sound) so adding another identical system and doubling everything is very satisfying. Of course it's easier to adjust the EQ since I can/must use the same for all speakers, but at the same time, the Denon auto EqX that everyone likes in Denons didn't work for me. It made an horrible sound, absolutely unlistenable at higher volumes so I had to de-activate it and go fully manuall.
The results is great for me, but I did have to spend countless hours adjusting everything and my best one for music listening has to use the multi-channel stereo wich rocks the house. It's not great in stereo only as it lacks deepness so I might try to plug Both Bose for lefts and rights instead of surrounds and heights but for now it's plenty good.
Sound with my older but more powerful Pioneer VSX-1018AH was traveling thru wall (I could hear basses and some low mids) from outside but now, I can distinguish almost everything so I'm gonna have to be careful not to bother neighborhood.
The Atmos/DTS X effects are really great but I will probably have to buy an Apple tv 4k or a Shield since none of my gear except htpc and PS3 handle it.
Here how it looks, with the black and silver speaker sets:
photos.app.goo.gl