You can either override all the settings in appserver/static/dashboard.css or create your own CSS file to be included in your dashboards like save your own copy of bootstrap.css and save as bootstrap-enterprise.css.
Could be that, not sure where the file comes from exactly.
It gets in our way by applying styles we then have to counter with other styles.
I get the idea that there is no way around this as any client that would download our app from the marketplace would have the bootstrap-enterprise.css file in their Splunk instance anyway.
See @niketnilay's comment. I asked which file because if it's one from the app or the one from the splunk base install determines if this is really an issue or not. The below comment captures the point I was getting at.