You want the chain straight, and you want the wheels aligned. When you have a choice between the two, I'd prioritize the wheel alignment. Wheel alignment affects everything in terms of the riding experience on the bike, from turning to braking/accelerating. Chain alignment (unless *extremely* off), is more related to chain wear over time. If the countershaft sprocket and the rear sprocket happen to be a mm or 2 further from the centerline of the bike, the chain might not ever be able to align with the exact straight line that you're shooting for between the wheels, as there is no cheap/easy way to shim them perfectly. But having the chain slightly misaligned really isn't that big a deal - the risk is slightly quicker chain & sprocket wear. But on a low-powered / low-torque bike like this, chain wear is going to be affected much more significantly by how careful you are to keep the chain lubed properly over time. Let it get dry and rusty, and it could be toast in a few thousand miles. Keep it adjusted and lubed, and it could last for tens of thousands of miles.
This is why I always thought the silly chain aligner tools that are sold to new riders are relatively pointless.
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