I would say it is a matter of preference.
I have had both (bare bottom and with substrata), and prefer sand over all else, except in my quarantine tanks, which are bare bottom.
I like my aquaria to be communities. That is simply not possible with bare bottom tanks, even if it makes some things easier. The fish are only one of the various types of organisms in a community.
The idea that is not possible to safely have FX6 filters in sand-bottomed tanks is just not true. I have two tanks with sand and an FX6 on each for years (125g, and 75g); both have additional filters as well. No problem. Concerns about sand lifted by fish?, adding prefilters (all my filters have prefilters regardless) is soooo easy. Not an issue.