[edvinbesic]

I agree, but would this still be the case if using it through Apple Pay vs swiping the physical card?

[ceejayoz]

Apple Pay won't override the merchant's point-of-sale system's configured accepted networks; for example, it won't help you use an Amex at Costco.

(It will help you if the merchant says "we don't take Amex" but their terminal actually does, though. Surprisingly common at small shops.)

[madeofpalk]

Yes. Amex is already on Apple Pay all around the world, and it’s only accepted at stores that accept Amex.