Which comes out of the bank's share, not the merchant's.
For example, the Odeon cinemas app or Too Good To Go (food app). I always assumed it must be because the merchant pays a higher fee for Apple Pay transactions.
I've never seen evidence of such, but there is certainly concern about becoming ever more reliant on credit card companies. So there can be an odd push to set up a first-party-account-based payment method (even if that winds up actually being backed by credit cards today).
The behavior doesn't always make immediate sense - for example, Walmart going as far as to special-order payment terminals without NFC so that they can never accept contactless, but then having you pay with their app - with a credit card online transaction, which I believe is a higher rate.
For some apps, it may be that they don't prioritize Apple Pay merely because they know only some browsers support it, and only some percentage of people on those browsers have set it up.