I have 3 MTs connect via Wireguard(WG) (all setup and nicely working), using RouterOS v7.1rc6
RT 1: 192.168.88.1/24 (plus 10.0.0.1/24 for WG)
RT 2: 192.168.89.1/24 (plus 10.0.0.2/24 for WG)
RT 3: 192.168.90.1/24 (plus 10.0.0.3/24 for WG)

Routing between the 3 routers is nicely working over WG, I connect to all of the routers, I can ping and manage (HTTP, shh etc.) them from the other networks (no firewalls between activated).

I would like to route all outbound traffic

• from 192.168.89.128 through RT 1 (192.168.88.1) using NAT and
  from 192.168.90.129 through RT 3 (192.168.90.1) using NAT.

All other traffic on 192.168.89.1/24 should use the normal route.
IP addresses would be hard coded in the device or via permanent DHCP addresses.

In IPsec on an AVM FritzBox (FB) I am doing this by simply adding permit ip 192.168.89.128 255.255.255.255 any in the configuration and I am done (though the FB is super slow for VPN/IPSec).
I have seen a couple of ideas but they seem to use the HW port for deciding which pass to use.

What would be the easiest and most flexible way to implement an IP based outbound routing via different GW in different subnet using NAT in this setup?

Sounds like a case where you need to do two things...
a. ensure 192.168.189.128 is routed through the WIREGUARD Tunnel
b. at the 192.168.188.1 router, internet traffic is routed back through the tunnel to 192.168.189.128

On the 189 Router
I would probably accomplish a. with a destination route and route rule
dst address=0.0.0.0 gateway=wgtunnel_to_188 route-mark=use188internet
route rule
source-address=192.168.189.128
action: lookup only in table
table=use188internet