Tec has both trade ships and refinery ships, different type of ship for each.

Advent would not have refinery ships, so when you switch it to refinery, the trade ships become redundent.

The Advent do not use refinery ships, so the refinery quota on extractors is meaningless. What Resource Focus does is increase the extraction rate of resources of all extractors in the gravity well the Trade Port (which is using Resource Focus) is in. Initially, Resource Focus increases extraction rate by 8%, but can be increased to 17% and finally 25% (upgrades are tier 7 tech). Since RF is based on a percentage of the current extraction rate, it has the largest effect on planets that have high extraction rates to begin with (those with high alleigance or extraction bonuses).

Just be wary you don't break your longest chain of trade routes, unless you absolutely need the increased resource income rate.

You can set each one to what you want. Once researched, Resource Focus shows up as an ability for each trade port.