Is there any quality difference between ImageMagick and Lightroom, when converting CR2 to JPEG in 100% quality?
There are two aspects to your question, because "converting" from RAW to JPEG isn't a simple thing — it's an interpretive process.
So, your results are likely be significantly different. ImageMagick just uses the rudimentary raw conversion from
The second question is whether "100% jpeg" means the same thing in both of these programs, and the answer there is "no, it doesn't". But, at that level, I'll be shocked if anyone can tell the difference visually even with very careful inspection. The filesize may vary, but there won't be any really meaningful difference.