Apple apps do bypass NEFilterDataProvider (used by application firewalls like Little Snitch), and the per-app VPN mechanism (using NEAppProxyProvider). Thus, per-app VPNs can't be applied to Apple applications, but per-app VPNs were never intended to globally intercept traffic. Claiming that Apple apps bypass (all) VPNs in Big Sur is deceptive - they only bypass per-app VPNs that were never intended to cover all system traffic in the first place.
Traditional VPNs that cover the whole system and route traffic based on destination IP (such as OpenVPN in UTUN mode) use the Packet Tunnel Provider in Destination IP mode. To the best of my knowledge, global VPNs routing based on destination IP (ie. non per-app VPNs) still route traffic from all applications, including Apple ones.
Traditional VPNs that cover the whole system and route traffic based on destination IP (such as OpenVPN in UTUN mode) use the Packet Tunnel Provider in Destination IP mode. To the best of my knowledge, global VPNs routing based on destination IP (ie. non per-app VPNs) still route traffic from all applications, including Apple ones.
See this for more details on the Packet Tunnel Provider: https://developer.apple.com/documentation/networkextension/n...