The retransmission agreements may include bundling of other HD stations, too.
Here in Seattle, we have KOMO (ABC) and KIRO (CBS) on Dish in HD, just by themselves.
Then, we have the other two network stations KCPQ (Fox) and KING (NBC) which have insisted that Dish carry minor stations that are also owned by the major stations owners. KCPQ and KMYQ are co-owned. KING and KONG are co-owned.
It's important for KCPQ that Dish carries it in Seattle, because the over the air signal is not available to large parts of Seattle due to the location of their transmitter (Bremerton). KCPQ carries the Seattle Seahawks football games, which people enjoy for those few times per year that the Seahawks actually win. As part of the negotiations a couple of years ago, KCPQ insisted that Dish carry their also-owned station KMYQ. There was a handbags-at-dawn fight that kept KCPQ off of Dish for a while (IIRC).
The owners of KING also own independent station KONG. KONG shows a lot of local sports, and is also used for overflow programming from KING. For example, a few years ago, KONG carried Seahawks pre-season games which KING couldn't carry due to the Olympics. KONG also carries an additional evening newscast at 10pm. While I don't remember a slap fight between KING and Dish, clearly they negotiated to carry HD feeds of both KING and KONG.
Who knows what the details of the negotiations were, but we ended up with six HD locals feeds, rather than just four.