Sorry for spamming again :D But this is really odd - in the mission that gives access to the Valk prototype, the player is allowed to leave the sector and repair. Isn't that a bug?

Some missions allow this, others do not. it depends on the mission and its creator. I beleive that the same can be found for the tpg test pilot mission (Which happens to give nothing atm); 1 and 2 fail on sector leave, but the 3rd I beleive allows you to jump out and repair (iirc).