Он опоздал не из-за пробки, а попросту потому, что слишком поздно вышел из дома.

Опоздал is the past tense, masculine singular form of опоздать.

So it tells you:

• the action happened in the past;
• the subject is masculine singular (он);
• the verb is perfective.

Compare:

• он опоздал = he was late / he arrived late
• она опоздала = she was late
• они опоздали = they were late

Because Russian past tense agrees in gender and number, the ending changes.

This is a very common Russian contrast pattern:

• не X, а Y = not X, but Y

So:

• не из-за пробки, а ... = not because of the traffic jam, but ...

It strongly corrects a possible explanation and replaces it with the real one. In English, the feeling is:

• It wasn’t because of the traffic jam, but simply because...

The preposition из-за meaning because of takes the genitive case.

So:

• пробка = nominative singular
• пробки = genitive singular

That is why you get:

• из-за пробки = because of the traffic jam

A useful note: из-за can also literally mean from behind in other contexts, but here it clearly means because of.

Yes, пробка has several meanings. It can mean:

• cork
• stopper
• traffic jam

In this sentence, из-за пробки clearly means because of the traffic jam.

This kind of everyday polysemy is very common in Russian.

Попросту means something like:

• simply
• plainly
• just
• for the simple reason

It often sounds a bit more emphatic or stylistically stronger than просто.

So:

• а попросту потому, что... has the sense of
  but simply because... / but quite simply because...

Using просто would also be possible in many contexts, but попросту gives the sentence a slightly sharper, more dismissive tone: the real explanation is very simple, nothing complicated.

That comma separates the two parts of the contrast:

• не из-за пробки, а ...

In Russian, не ..., а ... is normally punctuated with a comma before а.

So the comma is there for the same reason you would pause in English in:

• not because of the traffic jam, but because...

This is a very good question, because both patterns exist.

Normally, потому что is a single conjunction meaning because:

• Он опоздал, потому что поздно вышел из дома.

But in your sentence, the conjunction is split:

• ...а попросту потому, что...

This split puts extra emphasis on потому. The sense becomes something like:

• but simply for the reason that...
• but simply because...

The split is especially natural when there is contrast or emphasis, as here:

• не из-за пробки, а...
• plus the emphatic word попросту

So потому, что here is not random punctuation; it signals emphasis.

Yes. Слишком means too, as in excessively.

So:

• поздно = late
• слишком поздно = too late

That is different from:

• очень поздно = very late

So the sentence is not just saying he left late; it says he left so late that it caused the problem.

In standard Russian, when you mean movement out of a building or enclosed place, you usually use из:

• вышел из дома = left the house / came out of the house
• вышел из комнаты = left the room
• вышел из офиса = left the office

Using с дома is nonstandard in most standard Russian contexts, though it exists in some regional speech.

So for standard Russian, из дома is the correct choice here.

Because the sentence refers to a completed single action in the past: he left the house at a certain time, and that fact caused the lateness.

• вышел = perfective, completed action
• выходил = imperfective, process / repeated action / background action

Here Russian presents the reason as a concrete completed event:

• he left the house too late,
• therefore he was late.

So вышел is the natural choice.

Yes, often it could be omitted if the subject is already clear from context.

Russian frequently drops subject pronouns when they are not needed. So in context, you might hear:

• Опоздал не из-за пробки, а попросту потому, что слишком поздно вышел из дома.

However, keeping он is also perfectly natural. It can help:

• make the sentence clearer;
• mark a contrast with someone else;
• sound a bit more explicit.

Yes. Russian word order is flexible, but changing it changes the emphasis.

Your sentence puts strong focus on rejecting one explanation first:

• Он опоздал не из-за пробки, а попросту потому, что...

That structure highlights:

1. the wrong explanation: not because of the traffic jam
2. the real explanation: simply because...

A version like:

• Он попросту опоздал потому, что слишком поздно вышел из дома.

would sound different and would not emphasize the contrast in the same way.

So the chosen order is natural because it foregrounds the correction: the traffic jam was not the reason.