settoappu ha hayaku owaru ni kosita koto ha nai.

It is a set expression meaning:

• there’s nothing better than ...
• it’s best if ...
• the ...er, the better
• preferably ...

So the sentence is expressing an ideal or preferred situation, not a strict rule.

Literally, it comes from the idea that nothing surpasses X.

Because 終わる and 終える are different kinds of verbs.

• 終わる = to end / to be finished (intransitive)
• 終える = to finish something (transitive)

In this sentence, セットアップ is the thing that finishes, so 終わる is natural.

If you wanted to focus on someone actively finishing the setup, you could say something like:

• セットアップを早く終えるに越したことはない

That would mean it’s best to finish the setup early.

Because Japanese often uses the plain non-past form for:

• general statements
• future events
• preferred outcomes

In V + に越したことはない, the dictionary/plain form is very common. Here it means something like:

• it’s best if the setup finishes early
• the sooner the setup ends, the better

So 終わる does not mean present tense only. In Japanese, the non-past form often covers future meaning too.

早い is an i-adjective meaning early or fast.

To modify a verb, you change it to its adverb form:

• 早い → 早く

So:

• 早い setup = an early setup (adjective use)
• 早く終わる = finish early / end sooner (adverb + verb)

Here 早く modifies 終わる, so 早く is required.

That に is part of the fixed grammar pattern 〜に越したことはない.

So you should read this as one chunk:

• 終わるに越したことはない

not as:

• 終わる
  • some separate に

In other words, the に here is not the usual particle for destination, time, indirect object, and so on. It belongs to the expression.

越した is the past form of 越す, which can mean to go beyond, to exceed, or to surpass.

So literally, Xに越したことはない is something like:

• there is no thing that surpasses X

That literal meaning is useful for understanding the origin, but in real Japanese you should learn it as an idiom meaning:

• nothing would be better than X
• it’s best if X

Also, the fact that 越した is in the past form does not mean the whole sentence is talking about the past.

こと turns the preceding idea into a noun-like concept: the matter of ..., the fact of ..., or the thing of ....

Very literally, the structure suggests something like:

• As for the matter of X, there is nothing that surpasses it

But that is too literal for normal translation. In practice, it is better to treat に越したことはない as one set expression.

They are doing different jobs.

1. セットアップは

   • This は marks セットアップ as the topic: as for the setup...

2. ことはない

   • This は is inside the fixed expression に越したことはない

So the sentence does not have two topics in the same sense. The second は belongs to the idiom.

Japanese can have more than one は in a sentence when they apply to different parts of the sentence.

No. It sounds more like a general preference or common-sense judgment.

The nuance is closer to:

• Ideally, the setup should finish early
• The sooner the setup is done, the better

It is not as direct as an order, and it does not strongly imply obligation by itself.

Yes, at least a little.

• セットアップは makes setup the topic: as for the setup...
• セットアップが would focus more directly on setup as the thing that finishes

So:

• セットアップは早く終わるに越したことはない

  • sounds topical, general, or contrastive

• セットアップが早く終わるに越したことはない

  • puts more focus on the setup itself as the subject

In many contexts, both are possible, but は often feels more like a broad statement and が feels more like a direct identification of what finishes early.

They are similar, but the nuance is different.

• 早く終わるに越したことはない

  • the sooner it finishes, the better
  • sounds more like a general ideal or preference
  • often feels a bit more formal or set-phrase-like

• 早く終わったほうがいい

  • it would be better if it finished early / you finished it early
  • sounds more like advice or a recommendation

So に越したことはない is often a little less direct and a little more like stating what would be most desirable.

No. Standard Japanese is normally written without spaces.

So this would usually appear as:

• セットアップは早く終わるに越したことはない。

The spaces are often added only in teaching materials to make the structure easier to see.