It will make a difference if it is off. Can cause wing rock too. Even with the engine mounted directly under you still need to do lateral balance because most 3D planes have built in right thrust. So right there your engine is off to a side some.

Dont try to check lateral by grabbing the spinner because that will give your incorrect answer. What I do and works out pretty well is with the cowl off I find center point on firewall and mount string there. Maybe by a screw in firewall or by drilling a hole and looping around or what ever works best for you to attack string. Then on rear find center and mount string in rear with what ever method works for your plane. I also used a tall dowl and made a stand out of it. Then marked center on bottom and set plane on it.

Some people never check the lateral and fly them well as is. But it is always nice to have your plane balanced out as best as possible so it will fly smooth and straight. The rest is up to the flier to make it look good in air.