Did you run some tests?
The Convert Format doesn't use Expressions in the "Audio Conversion Options > Convert to this folder" setting. Perhaps it should.
The only control you have is to set the base destination folder using the "Convert to this folder" setting, and then set number of levels of the existing folder structure you want to use, starting from the lowest level. MC will then use those settings to build a new location.
i.e.
If the "Convert to this folder" setting is set to "F:\MP3", and the existing file is "F:\Music\[Artist]\[Album\[Filename]", then set "And create levels of folder structure" ticked on and set to 2, then the file created will be;
F:\MP3\[Artist]\[Album\[Filename]
But with a new file extension of course.
The "And create levels of folder structure" setting can be anything from zero up, but once the available number of folder levels have been fully used, nothing else will be added.
i.e.
If the "And create levels of folder structure" setting is set to 3 or above in the example, then the file created will be;
F:\MP3\Music\[Artist]\[Album\[Filename]
If you are completely changing the folder structure for the conversions, just use the above to put the new files in a unique location, and then use the "Rename, Move, & Copy Files" function to move them to where you want them. Just make sure you have the converted files set to be imported into MC so that you can use the RM&CF function. If that is a real problem, don't import the files, use the "Navigation Pane > Drives & Devices > Explorer" function to find the new files, and then move them using the RM&CF function.