It is technically possible to tweak files under the C:\Program Files\Flexera Software\FlexNet Manager Platform\WebUI\ directory to make UI changes like updating the logo or colors. It would be up to you to work out the relevant files to update for whatever you want to do. These are considered "internal" files and there is no documentation or formal support for modifying them. If you break it then you'll likely be on your own to work out how to fix it - so proceed gently!
I changed on test system the banner, and put on red, so that I know that I'm on test system
Change FNMS Header Background Color
Path: C:\Program Files (x86)\Flexera Software\FlexNet Manager Platform\WebUI\Content\
File to change: scaffolding.less
File with color definitions: variables.less
Also you should know that after you make update to a new version, you need to do again the modification, and as @ChrisG said, when you do modification like that you are on your own. 🙂