There shouldn't be any insoles with custom shoes.. that should all be built into the shoe itself. Different brands do it differently and there are different takes on the word 'custom' but I've used Rocket7 for the last 20 years and have helped dozens of ProTour pros get set up with those guys and in every case, whatever was in the insole they started with, that same stuff was just designed into the shoe itself so the the inside of the shoe is really just a thin lining of ~2mm high density foam to provide a little give, or in some cases can be just raw carbon for TT shoes and the like where you are seeking minimal frontal area or minimal weight.
You should be having this conversation in depth with your shoe maker and not trying to offset or compensate anything on your end without discussing it very explicitly with them. Ideally you should do foam box molding AND plaster cast of the foot to get the best possible fit and then I would send those to the maker along with your current shoes and insoles so they can see first hand all of the elements that you are after. I would also discuss the varus wedge with them to see if they think it better to design into the shoe or use a shim, you can put this right in the shoe, but using a shim gives you more tunability down the road if you were to want more or less.
The thing that I think generally surprises people the most about truly custom shoes is the perfect fit of the upper, which is why you need the plaster cast. You can achieve a perfect footbed through any number of methods, but for me the thing that makes my Rocket7's so amazing is the way that I can use absolutely any level of tension on the upper and they feel perfect, no pressure areas, rubbing, etc. The downside of this of course is that your feet end up changing shape over time and without all the added padding you have with normal shoes, you will notice this every 5 years or so!
Good luck
Josh
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