Anaerobic sealer alone works fine. Be sure you apply enough so that when the assembly is tightened, sealant squeezes out all the way around. This way you are sure there is enough on the surface to fill any deep scratches that are commonly found on the flanges.
Another tip: remove all 12 studs from the axle housing; clean on a wire scratch wheel. Chase the threads in the housing with a tap and blow clean. Reinstall the studs using high temp thread sealer on the threads. We have found that oil is far more likely to leak around the stud threads and find its way to the outside than it is to leak past the actual flange surfaces.
Always seems that over half of my studs back out (frozen nut on stud) so I do what you do, take them all out, clean, run a thread chaser on the nut end (not a die), and flush with brake cleaner (I wipe up the housing after) so everything is dry and super clean. Then I use the high temp locktite so the studs won't move once installed. Then mount carrier as usual. Be careful to measure stud length protruding to get uniform length for the nuts.
All in Air Force blue and black trim
1962 M37B1 rectangular window hardtop, converted to Hercules 4 cyl diesel-intercooled & turbo charged, 12V, disc brakes
1962 M116A1 Generator trailer
1962 M116A1 Pioneer tool trailer
1964 M101A1 3/4 ton trailer
I don't recommend lock-tite, can make a broken or stripped thread stud removal very frustrating in certain cases. The aforementioned thread sealer offers better sealing capability and moderate locking capability, plenty sufficient in this application.
Concerning thread depth; it's automatic if you are using the original studs or replacements that have the correct thread length. Run them down all the way tight against the stud shoulder. If replacing studs; BE SURE you are not installing new ones that are too long. NEVER use studs longer than needed so the ends protrude into a cavity in which rotating components are housed. Think ahead; if a rotating internal component contacts a protruding stud; you have just experienced disaster in a big way.