So how would these advanced jobs affect endgame gating, raid progression, and class viability?

Right now, Jobs are designed to be "specialized" versions of a class, meant to perform better at a narrower role, best suited to group and raid content.

Out by yourself, use a base class to have more options and abilities to mix/match as needed.
Out with a partner, still probably use a base class and throw in a heal.
Out with a group, use a job to maximize your contribution in your specific area (heal/dps/tank).
Part of a raid... this is where things get messy...

So lets say that Advanced Jobs are for raiding. They need to provide some incentive to unlock, level, and use over regular jobs. So the advanced job needs to heal more, hit harder, tank/control better, otherwise there is no point in using it over the normal job.
But if we make advanced jobs simply superior to normal jobs, then a player with an advanced job will likely never use the normal job again... why would they, its a weaker option. This would also cause a degree of player segregation in raiding, those who have unlocked and leveled their advanced job, and those who have not, and are therefore weaker raiders.

I suppose that IF advanced jobs must be the stronger options that a player has, then there should be a locking/usage limitation. For example, advanced jobs can only be activated when inside of a raid instance/dungeon (would be pseudo leveled somehow). This would still handicap newer people who do not have the advanced job leveled for raiding, but it would prevent advanced jobs from being superior for all content.