SMART has posted plans of the platforms at Civic Center and Downtown San Rafael. They’re fairly basic with a shelter and a few seats.
It’s important to understand that the arrival of the train in Downtown San Rafael is going to have significant ramifications on the current transit center requiring extensive reconfiguration. This will not only cause disruption but is also likely to cost a significant amount to Golden Gate Transit who own the transit center and who is responsible for covering the costs of reconfiguration.
Conceivably additional costs such as reconfiguring traffic signals may fall to San Rafael. The city already has a fairly tight budget not aided by unfunded pensions.