After reading Cort's impressive answer; I'd offer an alternative, to "nearly" perfectly sealed. Construct a cover that fits over the ship; as close as possible with the constraint of being only two pieces with a single seal between them (as small as possible). Or for practicality, as few pieces as possible with seals as obvious as possible. Make the cover of
glass diamond$^1$ and stainless steel. Then pressurize the gap between the cover and the ship to match (or very slightly exceed) the ship's pressure.
$^1$ added: The OP allows future tech; present tech allows us to deposit diamond film and use high pressure to create gemstones; presumably future tech will be able to make pure diamond windows and thick diamond films for the cover described.
The point here is to use some non-toxic commonly available gas (the most common are hydrogen, helium, oxygen, nitrogen, neon, in that order) to pressurize the gap between the cover and the ship wall. Neon is probably your best bet, it is non-toxic and chemically inert, meaning it forms no compounds (unlike nitrogen and oxygen which both form compounds), and has an atomic mass of 20 (vs. 1 and 4 for hydrogen and helium resp.)
As Neon outgasses from the cover, it can be scooped up for replacement purposes. This makes it a good "sacrificial" gas, i.e. we may leak neon, but we don't leak our oxygen and other special recipe of gasses inside the ship that sustain life comfortably.
To the extent that Neon ingasses to the interior of the ship; it is non-toxic and we can filter it out for re-injection into the gap (the ship walls can have ports for this; remember only the outer shell needs to have as few joins as possible).
The advantage of the cover is also maintainability; with just a few simple straight seals that are easily accessible, we can mount equipment there to monitor the seals for leakage and fix them with relative ease. Such equipment can operate in a vacuum; the communication can be by magnetic field fluctuation, acoustic or radio wave through the cover without penetrating it. The same goes for other sensory equipment the ship may require, or antennae, lasers, telescopes, dishes, armaments, etc.
Of course the entire outer cover is sacrificial, as well. In the event of damage by space debris it can be repaired; but because it is not pieces bolted together and has no "components" other than the single seal (or a few simple seals) repairs can be hard welds and permanently fused glass melted into place.
In dock near planets the neon gas can be depressurized and re-liquefied for storage (yes, neon of all elements has the narrowest range of temperatures for liquefaction; just a 5.5F degree window, but we have future science on our side!). Then the cover can be detached; perhaps stored in space while the ship heads to the planet surface. Of course the ship would still be constructed to be pressurized itself, and would suffice in an emergency (like the cover being breached by an impact that does not breach the ship's hull); but it can be designed with many components for maneuverability, landing, loading and unloading cargo or passengers and so on.