3.9 makes a little headway on that from previous versions. It will save the maximized window state.
The Linux edition has some sort of issue in the wx toolkit Bible Analyzer uses in that it will not always retain the splitter (window dividers) position on next start. Hopefully, that will be fixed in a future Wx release.
Our plans for version 4.0 is to be able to save layouts, among many other things.
Developer, Bible Analyzer
But to him that worketh not, but believeth on him that justifieth the ungodly, his faith is counted for righteousness. (Rom 4:5 AV)