My understanding is canvas also applies AA the rectangle lines still look AA just at a higher DPI.
It looks to me like the rectangles done in WebGL are drawn at the scaled resolution (1920 x 1080) vs the unscaled resolution (3840 x 2160), whereas the canvas is DPI aware and drawing at the full 4k resolution.
I would need to dig further but basically in WebGL the rectangles are drawn to a texture at the lower res then upscaled just like a straight image of a rectangle prerendered would be at the lower dpi.
Edit:
Looks like paper.js is specifically HiDpi aware and it can be turned off for better performance which would be more fair when compared to the other implementations:
hidpi="off": By default, Paper.js renders into a hi-res Canvas on Hi-DPI (Retina) screens to match their native resolution, and handles all the additional transformations for you transparently. If this behavior is not desired, e.g. for lower memory footprint, or higher rendering performance, you can turn it off, by setting hidpi="off" in your canvas tag. For proper validation, data-paper-hidpi="off" works just as well.
Also PixiJS seems to support HiDpi if resolution is set properly:
// Use the native window resolution as the default resolution
// will support high-density displays when rendering
PIXI.settings.RESOLUTION = window.devicePixelRatio;
