If your bike is bone stock, then we would hope by design (from the manufacturer) that by making the rear axle and the pivot bolt parallel (in effect that is what you are doing), you are then aligning not only your chain but primarily your rear wheel in aligned with the frame and therefore with the front wheel (assuming no frame bending).
With these wheel and swing arm conversion mods, one of the big tricks is to figure out where to locate the wheel in the swing arm and what spacers to use at the rear axle to insure the rear wheel is centered in the frame. Then the job that remains is also how to adjust the counter sprocket offset so that the chain is still aligned after the wheel is finally centered in the frame.
In this circumstance (which is the context of the thread) simply getting the wheel centered doesn't guarantee anything about chain alignment. Most of the chain alignment techniques are based on running a straight edge or a laser or a string if you will that is parallel to the rear sprocket and projected forward to the counter sprocket. If the projected line is offset at the counter sprocket from where it left the rear sprocket the chain is not aligned.
Now to add fuel to the fire, I have suggested that the counter sprocket can have runnout errors as they are partially supported in a rubber mount with only a 30mm or so central spacer/bearing to keep the sprocket carrier square with the wheel.
A sufficient method (which is independent of this sprocket runout) of insuring chain alignment (and no worse than the sprocket method) is to make sure the chain is parallel to the rear wheel (assumes straight wheel). This avoids any issue that might exist with runout and is sometimes simpler to measure.
