Using a 100A main breaker in a 200A panel
Breakers protect wires.   The wire to the sub-panel can only be protected by the breaker in the main panel, and that must be correct for the wire's type and size. 

Like Ed Beal says, you don't need a master breaker in a sub-panel.  The breaker in the sub-panel wouldn't protect the wire to the sub-panel. It protects the sub-panel itself, which is listed for 200A.  It can also be nice if you ever get sick of paying the tenant's electric bill and have the electric company feed a separate meter to that panel - voila, the master breaker is there already! 

(I'm saying "master breaker" to avoid saying "main breaker", which might be confused with "breaker in main panel".) 

If you are hoping for the sub-panel breaker to trip before the main-panel breaker, that doesn't work. Breaker trip curves are complex and unpredictable. 

If the 100A breaker is not listed or labeled to work in the 200A panel, then you cannot use it, end of subject.  That's the law. 

This is a situation where buying from a proper electrical supply house (and not a big-box home improvement store) will be very helpful.  You tell them what you want, they will sell you the right thing in the first place, and stand behind the combo.   On price, for the behind-the-counter stuff, I find them more than competitive with big-box. Their customers are, after all, electricians who deal in volume and drive past 3 big-box stores to buy there. (Electrical supplies do tend to wildly overprice the impulse-buy grab-candy at the front of the store, so don't go off those prices.)