IMO, this is a good reason to use a different subnet like this. There are other ways you could achieve the same end result (such as replacing your main router with one running OpenWrt and then using VPN policy based routing), but this one is perfectly valid.
That said, if you have a VPN running, you may need to do VPN-PBR anyway in order to allow the local traffic between your two subnets. That may be the reason you were having issues in the first place.
I think you can probably close this thread and start a new one if/when you have issues or want to change the topology.
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