In VOY episode "Thirty Days", they had the Delta Flyer reconfigured to go underwater.
Janeway stated it would take a few weeks to get Voyager ready to do that where as Delta Flyer would've been done in a few days.
If Starfleet was properly super prepared, every Starship would've been underwater and atmospheric ready.
But that's how I would run Starfleet. Be super prepared for everything. Not leave stuff to chance and improvization.
Improvization is done when necessary, but crazy preparedness is how our US military trains so they can deal with just about any situation.