So the computer's default settings need a tweak that nobody thought to give them. Not surprising, given the amount of work there is to do. (Though you fiddle around with the holodeck ALL THE TIME, but you can't change something which might be useful for ship's business?)
As for everyone using personal padds or needing to be at a certain location to enable something, it's security. The ship can be interconnected if necessary but isn't to mitigate the effects of system attacks and failures. As they are dealing with unknown, highly developed cultures all the time (some with tech they can't begin to imagine, let alone counteract), they need to be able to isolate systems from others. Otherwise, a tech savvy alien lightyears ahead of the Federation could exploit a flaw in the replicator programming and initiate the ship's self-destruct sequence.
Though to be honest, if they've reached that level of sophistication, they will probably be non-corporeal/have Q-level powers anyway...