I’ve only seen the Layer 3 Roaming with a Concentrator used once, and I’m trying to remember how it worked. From memory I believe you’re correct in what you’ve written.
When you configure the SSID you set the VLAN number, and this is the tag which is applied to the traffic as it exits the VPN concentrator MX. Between the MR and the MX it uses an IPSec tunnel between the management IP address and network of the MR and the IP address configured on the WAN1 of the VPN Concentrator MX. I think you may be right about the documentation being wrong as an MX in VPN concentrator mode has no idea what VLANs it has attached (unlike a MX in NAT/routed mode, which does).
The ‘difficult’ part is understanding the traffic flow for the SSID at the VPN Concentrator MX end when the traffic leaves the IPSec tunnel. In this regard my understanding is that the IP address on the MX is largely irrelevant - there is only one IP address on the MX, and it’s in the native VLAN, but you could have many SSIDs, with different VLANs terminating on it. Traffic receives the defined tag and is placed onto the network, essentially you create a VLAN that stretches from the MR all the way through the VPN Concentrator MX (which is effectively Layer 2 only) and out to the default gateway for the VLAN wherever that is (the MX100 in your scenario).
For traffic returning to the MR, sent from the default gateway for that VLAN (again, the MX100 in your scenario), there is no IP address on the VPN Concentrator MX for that VLAN. My understanding is that the VPN Concentrator MX will listen for, and forward all the Layer 2 frames into the IPSec tunnel for the clients in the VLAN that it has learnt about, essentially operating as a Layer 2 bridge/switch for the VLAN.
Now, if I’m understanding you correctly you’re essentially trying to separate the client traffic on the SSID, from the Meraki management traffic, IPSec tunnel traffic, and so forth that the VPN Concentrator MX is generating. In this case you’re on the right track. You’ll end up removing the .10 address on the VPN concentrator MX for VLAN100 and replace it with the IP address in VLAN10. The trunk between the MXs will need to have the native VLAN set to 10. And this isn’t going to be a seamless change or something you can do remotely, you’re changing the one IP address that the VPN Concentrator MX communicates with the rest of the world, and all the IPSec tunnels will need to re-establish. But it should be possible.