There are a lot of different approaches to D2. The "official" way to do it is with 3 minute rests, which are not counted towards the D2 time. Some people don't use the clock at all on D2, using it to really focus on form.
I do focus on the clock on D2, but try to maintain perfect form. I've started to use the rest times/round times as another indicator of progress and a way to mark incremental improvements between the big level jumps. I used to do roughly two minute rests, and then would meander back to the pull-up bar when my two minutes was up. More recently I've become much more strict. I did strict two minute rests until I got each round (L5) down to under 1 minute. Then I went to strict 90 second rests. Just last week I got back down to 1 minute per round with 90 second rests. If I hadn't leveled up I would have cut that down to strict 75 second rests next. As I get into level six I intend to continue the same approach. I'll start with strict 3 minute rests until I get each round down to 1 minute, then I'll shorten the rests and try to beat the time back down. But, again, for me, despite the clock, form has to be perfect for D2.