I feel like the conclusion from my comment should've been the other way around, but I'll give a general description of how the market is structured.
There's no clear-cut answer as to whether a publisher makes more from a copy of a volume sold being sold in physical or in digital.
The portion of revenue digital takes from each sale can range from 30% to as high as 75%, so there's a pretty wide variation. Meanwhile, physical stores only take about 20%, and even if you take into account printing and distribution cost, publishers generally end up with around 40-50% of each sale. In an ideal situation where a publisher can sell every copy it prints, physical sales are more likely to have better margins for the publishers. But the catch is that every unsold copy costs them money to store and/or dispose of the unsold copies.
That said, the publisher-run digital stores probably have the best margins.
Of course, how it affects royalties for mangaka is a completely different matter.
And while I'm at it, a few things regarding digital sales:
- Majority of digital sales are driven by backlog sales of old/out-of-print series and bulk sales from special discounts events.
- Generally for new releases of ongoing-series, digital only accounts for 10-30%, although there are exceptions.
- Unlike physical sales which has majority of the sales happening in first few weeks of release and then decaying rapidly, digital sales by nature are more a steady trickle that accumulates over time
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