Always that i have faced a situation with duplicated IP addresses TAC told me to avoid that. Many features look for the specific object into the data base using the IP address and it can end using the wrong object.
I think it is possible to get this working, but never had this scenario. I would try adding both remote vpn domains in one interoperable object, lets's say remote vpn domain A and remote vpn domain B. And make sure tunnel sharing is set to "per subnet pair".
Just make sure that on the first checkpoint gateway, the generated traffic is always with destination remote vpn domain A, so in phase two, checkpoint gateway will send the ID's --> "Your_Network - remote vpn domain A", and only that, it will not include remote network B, the ID's are based on the generated traffic. And the same on second checkpoint gateway, only traffic with destination remote vpn domain B should go through this gateway.
Of course you have to manage your internal routing correctly for both remote vpn domains, if these are adjacent networks maybe you will have to edit user.def file to avoid supernetting, take care of NAT, etc, etc. Again it is my personal opinion and never configured something like your scenario. HTH.