It affects "initial eligible" and "contract-expired/non-contracted" since 11Rs are missing from both tiers. Flying a new MWS via the cross-flow/interview programs can change your core AFSC and primary DT functional. For example, you're an 11R that gets picked up by the 89th. You're now considered an 11M and managed by the MAF DT (think IDE, DT vectors, and Sq/CC boards). On the flip side, say you're an 11M that interviews and gets picked up by the E-4/U-2. You are now considered an 11R by core AFSC and managed by the CAF DT. The aviation bonus program uses the core ID to determine who is in what "tier" based on retention goals. Therefore, bonus for 89th pilot...no bonus for U-2/E-4 pilot.
Another consideration in this is UPT. If you're an 11R that becomes a UPT instructor, you'll keep your core AFSC. This means that even though you're outside of an 11R flying community, you're still ineligible for this year's bonus based on the retention of core AFSC.