Ne izlazi iz vlaka dok kondukter ne otvori vrata.

Here it is an imperative: Ne izlazi = Don’t get out / don’t exit.

The form izlazi is spelled the same as the 3rd-person singular present form, so context matters. Because this sentence is giving an instruction, it is understood as a command.

Izlaziš is the 2nd-person singular present indicative: you are getting out / you get out. So ne izlaziš would mean you are not getting out, which is a statement.

For a command, Croatian uses the imperative:

• Ne izlazi = Don’t get out

This is about aspect.

• izlaziti is imperfective
• izaći is perfective

In negative commands, Croatian very often uses the imperfective:

• ne izlazi = don’t get out / don’t be going out

The perfective verb izaći gives the positive imperative:

• izađi = get out / step out

If you want a negative form with the perfective idea, Croatian often prefers:

• nemoj izaći

So in this sentence, ne izlazi is a very natural choice.

The preposition iz means out of / from, and it requires the genitive case.

So:

• vlak = train, nominative
• vlaka = of the train / from the train, genitive

That is why the sentence has iz vlaka.

No. In this pattern, dok ... ne ... means until.

So:

• dok otvara vrata = while he is opening the doors
• dok ne otvori vrata = until he opens the doors

The ne here is part of a normal Croatian structure and usually is not translated as English not.

Because Croatian is talking about a completed event: the point when the conductor has actually opened the doors.

• otvara = is opening, opens in an ongoing or repeated sense
• otvori = opens completely / opens once successfully

After dok ne, Croatian very often uses a perfective verb, because the meaning is until that action is completed.

Vrata is a plural-only noun in Croatian when it means door / doors. This type of noun is called pluralia tantum.

So Croatian naturally says:

• Vrata su otvorena = The door is open or The doors are open

In this train sentence, English might translate it as the door or the doors, depending on context, but Croatian normally uses vrata.

Because Croatian has no articles. There is no direct equivalent of English a or the.

So:

• kondukter can mean a conductor or the conductor
• vrata can mean a door, the door, or the doors

The exact meaning is understood from context.

Ne izlazi is singular. It can address:

• one person informally, or
• a generic reader in an instruction

For plural you or formal you, Croatian uses ne izlazite:

Ne izlazite iz vlaka dok kondukter ne otvori vrata.

Yes, Croatian word order is fairly flexible, but the original order is the most neutral and natural for an instruction:

Ne izlazi iz vlaka dok kondukter ne otvori vrata.

You can move parts around for emphasis, for example:

• Iz vlaka ne izlazi dok kondukter ne otvori vrata.

But that sounds more marked. For a normal warning or instruction, the original order is the best choice.