I havent been in the position to have custom shoes, but have researched it a lot. I eventually want to make my own when things settle down a bit with home building.

From what I gather, a good custom shoe will have you stand on foam to make a mold of you putting pressure on your feet. Then they will cast a replica of your feet and mold new shoes from there. So each shoe will have minor difference based on your personal anatomy. That is just my understanding as I have no real world experience in it, I do know there are people here who have so maybe they can chime in as well.

Yes and thats how mine will be done, casted with my foot resting on soft towel.
But if I am someone who pronates and/or has a knee that collapses in, and thus perhaps normally uses a varus wedge....do I build some of that support into the cast knowing that I won't have room in the custom shoe to jam in a aftermarket orthotic?
Or do I just make the cast of my exact foot, worry about varus support by using a cleat shim, and just forget about the arch/metatarsal support that my current specialized insole gives me?

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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Thanks Josh. I did discuss once already with the vendor, but it was more a discussion of "I want this, how do I do the molding to incorporate it", and we had a good discussion of how to do it. I'm just now questioning whether or not I should do it, or if that sort of defeats part of the purpose of the custom shoe - if you do an exact cast of your foot, do you no longer need the shape of a specialized insole also created in the mold.... I will def. discuss further with the vendor. Its a months long wait time, so lots of time, and have ordered extra casting wrap off amazon so I can do as many tries as needed at the casting... :)

Obviously your vendor will be the best source, but in my opinion its exaclty as you said, having to incorporate a insole defeats the purpose of a custom shoe.

Think about it this way, you use special inserts in other shoes to accomodate your foot and that is great, but that is to take a stock footbed and make it work for your foot. In having a custom shoe made, you are no longer starting with a stock footbed.