I might suggest that much of what you want with the translations to the final document via LaTeX is controlled by the specific packages, user-defined commands, and settings that you choose to use at the header of your LaTeX file. I suspect that Manuscripts will have a long way to go to be able to cover everyone's specific needs in some of this.
This being said, I certainly want formatting preserved across the entire document as it is set in Manuscripts. This means, anything that can put put in a \documentclass header to a LaTeX document should be preserved in translation Manuscripts->LaTeX-PDF. In addition, I certainly want to set my own header preambles via \usepackage, (re)newcommand definitions, and others. The subtleties of figure layouts is an entire world to itself. Even when I might use LaTeX directly, may answer to what you want will be different than yours. I would state therefore that figure layouts should be left to the higher-order approach of first creating a LaTeX document, tweaking it, and then generating a PDF.
In summary, the use of common standards for LaTeX export is important. However, Manuscripts will hopefully never try to be an absolute true-to-form front end WYSIWYG processor to a LaTeX document. Despite the long history of LaTeX, such tools do not exist in the mass-consumer market for a good reason, and it is not because folks who use LaTeX extensively do not want such a tool. LaTeX compilation goes well-beyond what can be done easily and reliably from a WYSIWYG word-processor. To get the truest-to-form LaTeX document output, you just have to work directly in a LaTeX editor, preferably one that has a WYSIWYG compiler built in to it. I certainly do.