The difference between the two Canon 100mm macro lenses are mostly: the L version has better weather sealing (doesn’t matter for copy stand work) and better and faster autofocus. The standard 100 macro is a really solid lens and optically I can’t really tell the difference. The price difference us usually about $100, but right not it’s a bigger difference of about $300.
Another option, if you plan to stick with an APS-C camera is the EFS 60mm macro. Optically it’s a solid lens for less than $400. The downside is that if you upgrade one day to a full-frame sensor you won’t be able to use that lens anymore.
I would NOT recommend the 50mm with extension tubes. I’ve shot with all three of the 50mm lenses from Canon and they’re great for portraits, but not suitable for camera scanning due to lens distortion and softness in the corners. That doesn’t matter for a portrait when the subject is near the middle of the frame, but it matters a lot for camera scanning.