We are also doing the same. My client has two sites. The design I worked out with them was each datacenter to have a single SSO Server to "control" the local vcenters at that site. This helped with DR as well as corporate growth when the company plans to have multiple DCs around the country and possible world expansion.
VCENTER authentication only needs SSO, thats pretty much it. Linked Mode and to a large degree SRM doesnt care for SSO. Multisite SSO during install only really helps in getting the SSO config up and running. Its as you said earlier, changes after that are manual between SSO servers.
Linked Mode between all VCenters with SRM is a no-brainer. It makes the licensing much easier especially where you are using the two sites as ACTIVE/ACTIVE. Plus you can Link VCENTERS regardless of the SSO its "connected" to. This gives a really good single pane of glass review of all your VCs and SRM.
Hopes this helps.
Thanks,
Boston Tech Guy