Because there's a lot going on at once and you've got drying time on the padding presses, the whole padding operation can be greedy on production space, which as like us, your space is tight, you probably find yourself moving stacks at various stages to make room for other jobs.
The Duplo DB-280/290 as you know has a 'PAD' option and if you can justify one for its primary purpose (perfect bound books) then I can see the attraction of putting a few ad-hoc pads through it, if you need them on demand when the Duplo is already heated up (that takes 25 minutes from cold)
However before considering the Duplo as a replacement solution for the traditional process, I would be exploring the cost differences.
In the UK 5Kg of padding compound is less than £25 whereas 5Kg of digital EVA glue pellets is upwards of £60. Whether coverage (number of pads produced per 5Kg of adhesive) is similar will depend on several factors of course.
Knocking up a couple of full padding presses and painting compound on them isn't particularly time consuming, and doesn't use any electricity, versus the half-hour warm-up, standby and production stages on the PB machine which do. You then walk away from the padding presses and return when they are dry and, as you rightly point out, the separation and trimming takes time. Although to get the finished edges you currently see, you'll probably still want to trim if you made the books individually on a Duplo PB machine. And of course, the DB-290 is only semi-automatic, so you'll be standing at the machine throughout.
I'd wager the old fashioned way is quicker, much cheaper and provided you're making a decent number of pads at a time (which you've indicated you are) also less hours spent on labour.
Perhaps just look at the times of day you're doing padding. As I eluded to earlier, for us, the frustration is the bench space it takes - therefore now we glue as the last job of the day, separate, trim and clear away first job the following morning. That works for us.
