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The ability to have your simulation code automatically update the data and figures in the manuscript is hugely valuable.

Another neat trick is a latex package called Catchfilebetweentags. This let’s you have a text file with named data fields that you can insert into your document, like when you want to state a parameter that was used in a paragraph. Generating that text file as an artifact of the rest of the data processing means, e.g., that parameters my paper says I used are the ones that I actually used.

Use minipages. I completely understand where you're coming from. But once I started using minipages I found that it is a great way to hack around almost all of these weird and uncommon placement issues.

>so I just export my results to latex format with pandas.

In other words, you don't do it by hand. I too rely on a tool to create my tables, which was my point. Doing it by hand is painful.