thank you for the excellent photos. that is the best way for us to be able to help you. your fitter has shown competence in the construction of your footbed, although trying to stuff an intuition liner with a footbed and a foot that appears from what the photos show to be beefy and wide, seems like it may explain where some of the suffering comes from. and even though it does look like he made some clean punches for width, they do not appear to be enough for your foot shape.
going back to my first post, this really helps to manage the variables. so here are a new set of thoughts based on your photo input. ok for the moment you can keep your boot fitter. however he has to come up with the correct answer in 3 areas.
the first is being able to accurately assess the range of motion of your ankle joint. if it is limited or tighter, or if it is hypermobile or looser could pose a big problem for the boot choice.
the second is getting a read on the height of your instep and the girth around your heel/instep perimeter. from the photo showing the partial rise of your instep, it looks to me like you are on the thick and meaty side. this presents a huge problem with your boot shell choice if your ankle range of motion is limited or tighter, because one of the fixes calls for elevating the heel and the roof of your atomic cs is too low to accommodate.
the third issue to address is the size, shape and location of your calf relative to the spine/cuff of the boot. this will be a problem for your quads and force undue pressure on the bottom of your feet especially combined with a meaty foot with a higher than average instep and girth.
the fix for these three issues are complicated, because depending on the outcome of the assessment, they will work against each other and if all three need attention the atomic cs is not going to work.
it is a 98mm lasted forefoot, with relatively low roof, with a fair amount of shell forward lean, and high straight spoiler.
now those are the big unanswered things that properly addressed will lead you to hours of skiing pleasure. in addition i will list below some of the problems that may be contributing to your pain.
depending on which model intuition liner that you have, and specifically if you have one that has the sewn in ultralon bottom which is either 9mm of 10mm thick, there is no way that a foot that appears to be as thick as yours can fit together in that lower volume shell with you, a footbed, and the 9mm bottom of an intuition. even if it is the model that has no ultralon bottom, you would still be hard pressed to get it in there with enough comfort unless you had a thinner, narrower, lower volume foot. and or your fitter padded the hell out of your foot to create more width and instep breathing room.
it also appears from the photos that your fitter has already ground the boot board down a little (possibly to give you more instep room?) the problem with this is that ramp angle of the boot board is critical to get you comfortably balanced over your feet, so we always want to deal with ramp angle before any fit work gets done. that is what i was referring to above with concerns about being able to achieve all of the necessary changes in an atomic cs that has a lower than average roof.
and just in case some of you bears think that i am bagging on the atomic, that is not the case, it is just pretty obvious that this model boot and the op's foot is not a love match. there are not very many bad boots on the market, however with the current lack of qualified boot sellers/fitters, there is a ton of bad boot matching that goes in in ski retail.
good luck getting this sussed out.