Re: Lowering a softail
Yes, and because the rear fork (swinging arm) is then 2" closer to the fender, it has 2" less to go before it bottoms out. The longer adjusters don't push the fork up: the weight of the bike just allows the frame to fall, relative to the swinging fork. Think about it like this: if you disconnected the suspension units completely, the bike would fall to it's maximum bounce setting, as the fork swung to its maximum travel, and hit the stops. That's taking 'lowering' to the extreme, and there's then zero suspension travel left.
Extending the adjusters doesn't reduce the travel in the suspension units themselves, but the limit of travel in the swinging fork is fixed, as if it went any further, the tyre would hit the fender.