It appears Doctrine 1 does not support this out of the box, so people are telling you to hook into the event that the Symfony CLI task system generates when it starts a new task (the loading of the fixtures). This would work, but I don't know whether this can load the value from the YAML value (maybe the regular "table creation task" would choke on the extra parameter?). The cleanest way to do this is to write a (little) subclass of the task that executes the Doctrine stuff, which understands an extra parameter you pass to the YAML file. This would first do the regular creation of the databases, and then set the autoincrement base values.
An even easier way (to implement, maybe not to execute) would be to create a separate file with the table names and base values, which is read by a new Symfony task you write, which creates and executes the necessary queries. Just don't forget to execute this task after you create the database but before you load the fixtures. And to update the configuration file every time you add a table.
The most quick-and-dirty way would be an extra SQL script with all the queries, and a shell script that executes everything in a row. But this takes the most maintenance on your side.