This is really frustrating - Shopify has spent years telling partners to use metafields for app data storage. The docs specifically point to app-owned metafields for internal logic, configuration, and workflows. There are even guides translating SQL concepts to Shopify architecture to push us toward native storage, and multiple docs showing JSON config stored in app-scoped metafields for Functions 
: Data modeling with metafields and metaobjects
If the concern is storefront performance, a more targeted approach would be far easier for app devs to handle, i.e a higher cap for JSON (for example 128KB or 256KB) or resource-specific limits (for example stricter on storefront-heavy resources, looser on order/app config use cases).
P.S. - The UI extension limit from 2mb to 64kb is also going to cause a lot of issues for many of us.