Hi Julius,
in my opinion it depends a lot on the case. If you can find standard Fiori applications that already provide main features you need, then I would advise to go with the first option and use the extension possibilities for further adjustment. Nowadays you can even adapt the UI of Fiori apps at runtime.
But if your customer's business needs are too specific and require big changes of the standard Fiori app, then developing your own custom one would make sense. You will be able to access it from Fiori Launchpad and there is no need to develop an additional login screen.
However, there might always appear certain functionalities that are available in Fiori Launchpad only for the most recent Fiori apps (or at least apps that follow Fiori Golden Rules), which you will miss in case you don't constantly catch-up with the latest features that SAP releases.
Regards,
Tsovi