Golden Gate Transit always has had 3 bus operations with distinct characters:

Commute - those expresses that run around a neighborhood or town in the early morning then jump on the freeway and HOV-it into SF (and vice versa PM). Nominally funded only by fares and bridge tolls. Inherited from Greyhound in concept, and some of the Marin commute routes probably still are pretty close to what the Greyhound routes were.

Basic Service - most transit lines would call these "limited stop" or "main line" because once they leave SF they mostly make only freeway stops until they get to their local zones. Funded like all conventional transit with a combination of sources including federal and state operating subsidies, bridge tolls, local subsidies from the counties and possibly cities, and of course fares. Also inherited from Greyhound, though over time the specifics have changed considerably.

Local Service - within a single county. GGT has always provided this in Marin, with a varying county subsidy (along with other conventional transit sources) and contract, but never did much in Sonoma. Marin toyed with setting up its own transit system and firing GGT several times, but never seems to have completely done that. Sonoma did, of course, set up its own intra-county transit system and cut GGT off from that particular funding pot. GGT still doesn't carry passengers between points completely within the cities of Santa Rosa or Petaluma - those towns have always had their own bus lines so GGT can only accept traffic to or from points there and outside as had been the case with Greyhound.

Why mention all this? Because the only service GGT provides that might be directly affected by SMART is the Basic Service, which unfortunately is probably its biggest moneymaker (or at least its smallest money loser) due to the variety of subsidies available. GGT will still run the rest, as they do now, possibly with minor modifications to connect with SMART where appropriate. And they will still have to run a modifed Basic Service anyway to cover times when SMART doesn't run (Will SMART run hourly or better in both directions from 4-5AM to after midnite? GGT does and will still have to.) and places SMART won't go (Southern Marin, for instance). SMART also will never provide the distributor service from the ferry that GGT does, though someday perhaps it might get close enough to the terminal that a transfer can be by walking (may need a moving slidewalk like the ones in airports for ADA reasons) rather than another shuttle bus. The main thing SMART relieves them of is the railroad r/w north of Corte Madera and perhaps a small percentage of its Basic Service. That doesn't reduce GGT's operating cost much, but does reduce the ridership (and its subsidy, probably in a greater proportion than the ridership, because FTA won't continue subsidies for "competing service" after the train starts up) for the Basic Service.

So I don't see any reason why GGT should welcome SMART with open arms, or even with gritted teeth, at least until it gets close enough to deliver a decent number of passengers to the Larkspur Ferry. Or unless SMART can share enough money to patch the holes poked in GGT's budget.