By default in Anki, you can set up custom servers to use as the target for syncing.
Would you consider allowing users to use their preferred cloud storage, such as iCloud?
iCloud has end-to-end encryption even for application syncing like Anki. This way, users can sync their platforms while still having complete control over their data and its encryption.
I won’t address that first comment since it’s mostly speculative and doesn’t really articulate any challenges.
As for the second comment, I can respect that Anki needs to work on more than just Apple devices, and I also think it’s fair to acknowledge that the platform is charged for on Apple devices. Rather than uploading/downloading the entire collection, there are better alternatives.
Currently, with AnkiWeb, there does not need to be a complete re-download/re-upload on each sync. My proposal is to have a custom server instance like the Anki manual describes creating, but have its filesystem on iCloud. Then have each platform (iOS, Mac, whatever) spin up that server locally, connect to itself, and then perform the sync operations.
I think this solves all of the listed concerns, but may generate other ones.