Ignoring Limitations

Dog Fight: Starship Edition ignoring limitations
Dog Fight: Starship Edition ATTACK card Clear Shot ignoring limitations
What is the difference between ignoring obstructions and ignoring line of sight?

Line of Sight is the broader category. If you can ignore Line of Sight limitations you can see objects that would otherwise be invisible to you for any reason. This includes ignoring obstruction limitations.

Obstruction limitations are a subcategory within the general line of sight concept. An object could be blocked by an obstruction and still be visible to you if you can ignore obstruction limitations. But if that same target has the STEALTH ability, ignoring obstructions won't help you because you would have no line of sight to it anyway.

Obstructions (on the map) only block visibility because an object is in the way. Line of sight limitations (the phenomenon of visibility) can make something partially or entirely invisible, not merely blocked. Some cards state you can ignore "obstruction limitations" which applies to the obstructions on the map. Line of sight limitations require a bit more to overcome.