There are lots of alternate character ranks in IH and RH that your character can take. However, can those alternate ranks still be taken as alternate ranks during ascension level Ranks 9-16? For example, could a Magos achieving Rank 13 still choose to become a Mechanicus Secutor? Could a Death Cultist Rank 10 choose Tyrantine Shadow Agent as his Rank 11 alternate rank? A Rank 15 Sage decide to become a Saboteur instead of just a plain Rank 16 Sage etc?

You should go case for case. In the concrete situation of the Mechanicus Secutor, it's irrelevant since one of the first talents he can get at rank 9 gives him everything and more that career could.

But if you really wanna get those background packages, then do the character from rank 1 to 8 nad then apply the transition to rank 9, spend te extra 500 XP and start playing.

I think the question was something more along the lines of if a character has already ascended and then decides they would like to take an alternate career rank at, say, rank 11.

I personally would consider allowing this if the alternate rank fits in with that character's story. Since an Ascended character is offering to sacrifice alot of high-powered skills, talents and influence for this option it puts alot of weight behind that player's request in my mind.

Of course since Ascention has much higher XP costs for things I would definately increase the cost of going back and "elite advancing" things from the missed rank. Adding 50xp to something that costs 1000xp just seems laughable.