One thing for sure, the cartridge body has got to be sandwiched in the strut tube between the bottom and the nut, down tight!
Some cartridges may or may not come with lower end spacers to properly center up the bottom of the cartridge.

If I read this right, you now have play of the cartridge body(s) up & down in the tube or you cannot get both nuts to now "thread themselves all the way into the tube" to lock the cartridge down solid.

If both cartridges bodies are identical in lengths. Then something gave way down at the bottom of the strut used for support of the original one also.

Or we need to define your term "will seat fully" when torque down? If you are expecting all of the threads of the nut to disappear down into the tube, that is not suppose to happen. The hex part will be sticking up away from the end of the tube and up probably 3/16 of an inch away.

The inner part of the gland nut has surface machined to fit the top contours of you specific cartridge housing. That crimped end may vary with each manufacturer and is the reason they are stressing using those they have supplied.

Make sure as you tighten in the cartridge that you keep the chrome rod centered in gland nut until there is no side shake. By then you should not be able to pull the cartridge up or down.
Then you will want to pull that nut down as tight as you can get. I use a pair of groove joint pliers with about 14 inch long handles to tighten it. Both arms and shoulders yank should do it.

Another thing I got into was replacement dust boots. I found that KYB and AutoZone sell boots. The KYB's are about twice as much as AZ's China brand but they look identical. Both are a plastic type but KYB's are slightly more softer and was stamped made in USA. Even though I believe they are a Japanese outfit. Things are just about packaging it seems.
The next thing is neither of them seals at the bottom at all by about 1/4 inch all the way around. This ticked me off. Planned deterioration of the cartridge seals.

I went to Home Depot and bought a 1&1/2 pipe rubber drain line connector for about $3.50. They came with two stainless steel gear tooth type clamps but I did not use them.

I cut the connector in-half to get a rubber sleeve to fill the gap for both strut housings boots. I used nylon wire ties to secure the boot down as the boot kit does not come with them either. One could probably not use them as they were nice and snug.
The top of the boot cover fits just loose enough around its own grooved rubber bumper that if any amount of compression of air volume inside will equalize very quickly. If that is a concern for anyone its not that tight to do anything noticeable.

I just had to deter that whirl wind of dirt and water from having its way with those seals on the chrome of the absorber. I have been eyeballing my rear shocks for a filler but those covers come way down on the absorbers tube body. May not be an issue.

Hope you figure out you dilemma as I did with the boots.

Phil