As far as I know, the ranks are the same as vanilla, just renamed. See
here.
Not sure how rank limits interact with rankless agents (dogs and the like), and whether the overall rank limits are true in OXCE. Never had cause to go over those mentioned in UP. I assume rankless agents don't count, because I have 5 colonel equivalents and 125 ranked agents out of 188.
What is this 'Special Agent', anyway? Do you mean 'Senior Agent'?
I don't know why your rookies aren't getting ranked up. You don't have 'field promotions' on and leave them at the base or something? Otherwise, maybe it's this "...may not be given with high troop counts." Never run into this myself, maybe someone familiar with the code knows?
You can only have one 'Chief Agent', as always, so that's normal.
A larger pool is definitely useful. At least 250 are needed to 'max' your agents' ranks if the limits mentioned in Ufopedia are valid.