You may still run into unconverted components sometimes when you advance in tech between getting them and eventually using them, but that's an edge case.
An important one though. Maybe the original idea of converting them manually is best. I could add a 'Modify for Use' button to the Stockpile window (alongside scrap and disassemble) and highlight the eligible ones in a different colour (like green for those will generate research points). Plus another button and colour for those that could be researched.
The manual option has my preference.
So those that want to use it, can and others can ignore it.
I always dismantle or scrap alien components. Never use them.
As a sidenote:
Personally, I've always found it weird that when we salvage a ship we immediately know which component it is and all its attributes. Together with knowing how to use it.
I've got the same feeling about "boarding" ships from another alien race and being able to fly it away with zero knowledge about how the aliens technology works.
But I know that the current implementation might be a gameplay abstraction.