As always I'm a little slow getting to this and DW has used up all the good answers
You can form the insole by wetting and using a press to get the insole securely against the last. Next you can use cork to fill in the "negative space" on the insole where the met pad etc. would be. An other option is to take some questionable quality kid skin that you really can't use for much of anything, rubber cement it to the last and build an insert from cork, it will feel more like a Birkenstock. Next grind and shape the insert, than take it off the last and clean the last of any glue residue. (don't forget this step or you will have the hardest time getting the last out. It was a prank that was played on me when I was the new kid in the shop) Put talcum powder in between the last and the insert and lay a thin leather insole on the bottom, nail in place with 2 or 3 tacks and make the shoe as you would normally do. The bottom of the insert can be flat or slightly rounded as a normal production last would be. This way you can remove the insert once the shoe is ready and make adjustments or replace it before the shoes wear out. You could make the shoe directly over the cork but it's probably not strong enough to hold it's shape once you get to resoling number 2 or 3.
Just another way to doing it. This technique will typically add a little bulk to the shoe but the insert does not have to be thick and can even be 3/4 length.
BTW nice job on those tall moccasins you posted the pictures of in the gallery. I'm intrigued by the sole. How durable is this? Do you apply multiple layers of barge and grindings, slowly building it up or all at once with barge that has gotten harder from what it would be out off the can?
Do you happen to have the recipe for the tanning process? How was that leather to work with? Anyway I wanted to compliment you on that but had not gotten to it.