Is that really a problem as long as Synology supports it (we're paying money, after all)?

So far it hasn't but it does mean we dont get up to date BTRFS version. Which is what worries me most.

Are you sure? Synology do a very bespoke BTRFS and backport a lot, even though it's incredibly complex to do so. Their BTRFS is not standard, or rather it's not the standard version for a given kernel version.