It could be many things. Yours may be different from my issue. With yours, leveling on the ends of the tubes, especially small diameter but short span, may not be accurate. What matters in your case would be a level across the side of the head tube, versus a level across the side of the seat tube, however in both cases there can be local distortion due to welding. Fortunately, neither is tapered, so you should easily get readings.

I have the same issue symptom, canted handlebar, but perhaps different cause:

I have a Dahon Speed P8. The 2-piece handlepost was recalled. I bought it in to the local Dahon dealer, they replaced it in 5 minutes (they did not replace the entire handlepost, just the lower, so just raised the upper and handlebar and swapped the lower). I loaded it in the car folded and took home. Next day I unfolded it and could tell the handlebar was canted. I eyeballed from behind and could easily see the handlepost was not aligned laterally straight with the seatpost. Was not like that before. Bike was virtually unused. Bike shop would not replace again, and had already recycled old part. I looked carefully at handlepost base; It did not sit evenly on the headset, the bottom was flat but slightly canted so a gap on one side. Even if I were to machine the bottom half of the hinge to sit flat, the angle would still be off; The bore that clamps around the steer tube is off. My guess is the bottom part of the hinge is forged with the bore roughed, then final bored on a fixture, and the machinist was careless and a metal chip was between the workpiece bottom and the fixture on one side, so bore is not 90 degrees with the base. Dahon corporate also blew me off.

I publicized the matter on here, and one of the members at the time, who I thought was only a dealer, but now know they were associated with Dahon, sent me a replacement lower handlepost. I put it on. It was off-angle in a different direction, again, sloped gap between base and headset.

Here is my knowledge from the auto industry: Parts that fail production tolerance are set aside and sold as service parts. Even when you buy "OEM" parts, you are often getting "aftermarket" quality. To see two service parts both exhibiting the same quality issue, and even varying in different direction, is clear proof.

Bike still sits in storage, I bought it for someone to use and they never did. Eventually I'll replace the handlepost with an aftermarket one that is higher quality than the OEM one, Dahon's one. Oh and as I recall, the color was off too, instead of pure black anodizing, it was like dark bronze or copper in sunlight, I've occasionally seen that on other Dahon parts with age. Finish defect, clearly not intentional.