I've written a long series of post about setting up IPsec VPNs between NATed machines. As you've already seen, with some creative configuration it's possible, but is it always worth the sacrifice? Sometimes performance requirements, or lack of support for anything else on the other side make it necessary, but if the other side is also a VyOS, or another open source system, there's an alternative.
While OpenVPN is usually associated with road warrior VPN setups, it is not limited to it. It does have a site to site option and it's very quick and easy to setup. For some strange reason, that option is neglected by just about everyone who otherwise supports OpenVPN: in OpenWRT and OPNSense it's possible to setup through custom config options, while in Mikrotik RouterOS it's not possible to setup at all. In VyOS we have an explicit option for it.
The advantages are that it takes very few commands to get a tunnel to work, and that it will work in any network where you can forward a single port, even is both sides are behind double NAT. The downside is performance: squeezing even 100mbit/s of encrypted traffic out of it can be impossible, typical iperf figures are 10-20 mbit/s. For many use cases that performance is more than enough, though if you plan to use the tunnel for storage replication or another high-traffic job, that option is definitely not for you and you'll have to resort to IPsec.