Is there a way to use the native discount system in Shopify Plus where I can create a %-Off discount for a customer to use, but have it limited to a max of 2 items in the cart? So if a customer ads 3 items their cart but the % off order will only be taken off 2x and the third will be regular full MSPR? Looking for a way to work this out without having to use a customer script.
Short answer No.
You can do that with the script editor app which is available for shopify plus accounts.