No, you understood it right.
These are the kind of things that hinders adoption of Mikrotik by intermediate level users.
The solution would be to mark traffic on the incoming interface(s) and src-nat by marked traffic.
(A) takes care of masquerade out the router.
sourcenat masquerade out-interface=wan1
sourcenat masquerade out-interface=wan2
(or sourcenat masquerade out-interface-list=WAN)
(B) takes care of ensuring ethernet5 to the interenet uses WAN2.
ip route primary ISP
Ip route secondary ISP
ip route secondary ISP route-mark=wan2
Please note that internal src-nat is a typical need also when a accessing (managing) non-routed networks / subnets over VPN etc, while wanting to retain traceable logs of entering and exiting traffic.
Traffic enters via management node vpn interface from a remote subnet which is not available via the local subnets default gateway. (instead of doing src-nat at remote subnet)