Starships and submarines both operate in extreme environments where the crew must be sheltered.
And spaceships don't?
Spacecraft, in the modern sense, are more like aircraft than starships.
What modern space craft other than the shuttle bears ANY resemblance to an aircraft?
Actually, every Russian space craft since Vostok--with the singular exception of Buran--has been designed almost EXACTLY like a conventional minisub.
The Apollo missions were each only days in length. The Space Shuttle doesn't stay aloft much longer than that.
So "isolated, a discrete distance" you actually mean "two days travel from the nearest human settlement." And since the Apollo missions only flew a hundred and 186 thousand miles from anything RESEMBLING safe harbor, that doesn't count.
And all manned spacecraft and space stations from Earth to date are typically in constant contact with their "mission control" HQ. Those are stark differences from the starships depicted in TREK.
It's also a stark difference from every naval vessel put to sea in the past sixty years. Even submarines are not more than six days away from a friendly port at any particular moment and not more than a radio signal away from a command base. Compare this to early TOS episodes (and even a few TNG episodes) where a message sent to Starfleet are described as taking several hours just to REACH them. That is a condition entirely unique to space craft, especially to REAL space craft, which--BTW--includes unmanned probes.
By all rights, the Enterprise is built flown and operated, basically, like a gigantic manned version of the Cassini-Huyen's spacecraft. It's designed to operate autonomously for years (naval vessels are not; even submarines make a port call every three to six months). It had its own small auxiliary craft for close range surveys (submarines do not, aircraft carriers do not carry scientific probes as standard equipment). It had a vast array of scientific sensors and monitoring equipment (submarines and naval vessels do not). It had the communications gear needed to send information it had collected across interplanetary distances back to its point of origin (even aircraft carriers would be hard pressed to transmit as far as the moon). In point of fact, if you took a shrink ray to NASA's mission control center (compacted it to the size of a matchbox, let's say) mounted it to the side of a probe and shot it into space, you would at that very moment have a manned spacecraft that does EXACTLY what the Enterprise does, in EXACTLY the same way, with the only missing component being a working FTL engine. In this single criterion, the only functional difference between a starship and a modern space craft turns out to be SIZE.
V'ger seemed to think so as well, thus encountering the Enterprise it immediately believed it had discovered another living machine fundamentally similar to itself. To V'ger, Enterprise was just a probe with things living on it; at the end of the day, that's all a starship really is.
I say again: by METAPHOR, the comparison works. But by environment, by mission and design specifications, by technological requirement and any other material category, there's no getting around the fact that the Enterprise aint a submarine. Repeating again: you might as well be comparing the SeaQuest to a space shuttle.
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