I've installed literally hundreds of sets of Koni inserts and never once had the problem you are having..... therefore one must conclude you are doing something wrong or your shock tubes are bent maybe, either way the problem appears to be unique to your car.
Have measured the inserts and they are 6mm to long for the casing.
Have checked the part numbers for the inserts and are correct.
The casings are toyota ones not after market replacements.
Have now filed the bottoms of the shocks by 6mm. There was a sort of nipple on the bottom so have removed a bit of this to make them fit. Now the large flange nut now does up tight with a 4mm gap between the casing and nut.
My first set of rear KYB inserts didn't fit; they were too long for the strut casings and too narrow. I assumed I was given Mk1A items instead of the Mk1B inserts I needed.
On explaining the problem to the supplier and my theory as to why they didn't fit they sent me replacements that that did. I had no problem with the fronts though.