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Not sure about align-honing the way you would do with an engine. However, any cap should be properly fitted to have the right "tightness" on the races/bearings that it clamps down.
You'll find details in some of the more popular differential rebuild links on here.
Also, I am just having my whole differential strengthened and rebuilt mainly with Tom's Diff parts. The only item I did not go for was the upgraded cap as it seems that something else would break before that part. Might be a nice insurance, of course....
The steel cap always has to be fitted. Depending on the housing it could require a minor touch up to major machining. The cap is good upgrade for the 12 bolt conversion that Gary and I will both be doing but you will almost always blow up the stock 10 bolt carrier before you break the stock cap.
Mike