..this release is similar to iOS 3.2. (3.2 was iPad-only, 4.0 and 4.1 were iPhone/iPod-only, and 4.2 finally unified the two branches.)
My guess is that iOS 3.2 for the iPad was a fork of an earlier version of iOS, worked on by a separate group of people than those that were working on iOS 4.0 for the iPhone[1]. The split was because it took a few months for it to all be merged back together in a stable way, not for any big strategic reason.
1. Remember, the iPad was a big secret - even within Apple.
Even though the secrecy around Honeycomb doesn't compare to the iPad, Google still does Android development in secret. Privileged hardware partners get to participate in development of the next release before it's revealed to the public (or even to other handset makers).
Aside from secrecy, there are other reasons (like product schedules) that Honeycomb may have been developed on a branch, concurrent with Gingerbread development. Previous releases like Cupcake and Donut were developed on long-lived branches, with frequent merges from the AOSP mainline. The end result could be the same, even if the rationale is slightly different.
My guess is that iOS 3.2 for the iPad was a fork of an earlier version of iOS, worked on by a separate group of people than those that were working on iOS 4.0 for the iPhone[1]. The split was because it took a few months for it to all be merged back together in a stable way, not for any big strategic reason.
1. Remember, the iPad was a big secret - even within Apple.