I am mainly a web developer learning Java and currently, I am working on FXML.
There are a lot of possibilities in terms of positioning and styling like the panes, but since I am familiar with CSS I was wondering if it is a bad practice to do everything in CSS instead of using panes like you would in HTML.
Are there any downsides to this?
Check out Scenebuilder. It will autogenerate some css for you to play around with.
In general, no, it's not bad practise to use css as freely as you would in HTML.
However, you do not have the flexibility of using margin-left:calc(50% - div-width/2); and similar tricks.