Right now there is no way to use ApplicationSearch with Workboards/Maniphest. This would be useful to explore
Yeah, T418 is "customize stuff".
We're not currently planning to implement a query-by-column, because columns with the same name on different boards aren't instances of a single object. It would essentially be "query by column name", which is a pain to implement and use, and renaming columns would silently break queries.
After T5474, you'll be able to write column triggers which (for example) add or remove projects or set custom field values when tasks are moved to a column. If you want to find all tasks that are "In Progress", you can have your various "In Progress" columns set a "Task State" field to "In Progress", or add an "In Progress" project. Then you can search for the tasks by searching for this field or project.
It's possible we might do "in columns named: ..." eventually, but I want to do T5474 first and see if that covers it.