Learn Hardcore French: Le tram dans lequel elle s'assoit d'habitude est presque vide le dimanche. - The tram in which she usually sits is almost empty on Sundays.

Because tram is short for tramway, which is masculine in French: le tramway.
When it’s shortened to le tram, it keeps the same grammatical gender (masculine).

So you say:

le tram, un tram, ce tram, dans le tram, etc.

Why do we say dans lequel here? Could we use où instead?

Dans lequel is a relative pronoun meaning “in which” and it agrees in gender and number with tram (masculine singular).

Le tram dans lequel elle s'assoit… = The tram in which she sits…

Yes, you can very naturally replace it with où here:

Le tram où elle s'assoit d'habitude est presque vide le dimanche.

Both are correct. Differences:

où is more common in everyday speech and feels lighter.
dans lequel is a bit more formal and explicit, and it’s especially useful when the preposition isn’t à or dans (e.g. la ville près de laquelle…).

Why is it s'assoit and not just assoit? What is this se doing?

The verb is s'asseoir = to sit (down).
It’s a pronominal verb (with se, which becomes s' before a vowel).

You must include the reflexive pronoun when conjugating:

Je m'assois (or je m’assieds) – I sit
Tu t'assois
Il / Elle s'assoit
Nous nous assoyons
Vous vous assoyez
Ils / Elles s'assoient

Using just assoit without se is wrong in standard French in this meaning. You need s'assoir / s’asseoir to mean “to sit down”.

I’ve seen s’assied instead of s’assoit. Which one is correct?

Both forms exist, but usage has changed over time.

There are two accepted conjugations of s’asseoir in the present tense:

asseoir-type (traditional, now considered more formal or literary):
- je m’assieds
- tu t’assieds
- il/elle s’assied
- nous nous asseyons
- vous vous asseyez
- ils/elles s’asseyent
asseoir / assoir-type (more common in everyday speech):
- je m’assois
- tu t’assois
- il/elle s’assoit
- nous nous assoyons
- vous vous assoyez
- ils/elles s’assoient

In your sentence, s’assoit is perfectly correct and very natural.

Why do we say elle s'assoit d'habitude and not elle assied d'habitude?

Two reasons:

Reflexive form is required
To mean “sit down,” French uses the reflexive s’asseoir.
asseoir without se usually means “to seat someone / to make someone sit”:
- J’assois mon enfant sur la chaise. = I sit my child down on the chair.
The common modern form
In everyday French, for yourself you say:
- Elle s’assoit or elle s’assied = She sits (down).

Elle assied would mean “she seats (someone else)” and sounds strange here.

Why is it d'habitude and not de l’habitude?

D'habitude is a fixed expression meaning “usually / as a rule / normally”.

Literally it comes from de + habitude (without article), so we say:

d’habitude, not de l’habitude.

Compare:

D’habitude, elle prend le tram. = Usually, she takes the tram.
Elle n’a pas l’habitude de se lever tôt. = She is not used to getting up early.

In the second sentence, l’habitude is a regular noun (“the habit”).
In d’habitude, it has become an adverbial expression meaning “usually”.

Where can I put d'habitude in this sentence? Is elle s'assoit d'habitude the only correct position?

You have some flexibility. All of these are correct, with slight differences in emphasis:

Le tram dans lequel elle s'assoit d'habitude est presque vide le dimanche.
Neutral, very natural.
Le tram dans lequel elle s'assoit est presque vide le dimanche, d'habitude.
Puts “usually” at the end; sounds a bit more oral / conversational.
D'habitude, le tram dans lequel elle s'assoit est presque vide le dimanche.
Emphasises “as a rule / generally speaking” at the start.

Inside the verb phrase, d'habitude normally comes after the verb:
elle s'assoit d'habitude, not elle d’habitude s’assoit (which sounds unnatural).

Why is it dans le tram (“in the tram”) instead of something like “on the tram”? Isn’t it “on” in English?

French and English use different prepositions for transport.

In English you say: “on the tram.”
In French you say: dans le tram or en tram.

So:

Elle s’assoit dans le tram. = She sits (down) in the tram.
Elle va au travail en tram. = She goes to work by tram.

You wouldn’t say sur le tram unless you literally mean “on top of the tram” (on the roof).

Why is it est presque vide and not something like a presque vide?

Être is used here because vide is an adjective describing the state of the tram:

Le tram est vide. = The tram is empty.
Le tram est presque vide. = The tram is almost empty.

A vide would use the verb avoir (to have) and doesn’t work with vide in this meaning.
French uses être + adjective for describing states and qualities, just like to be in English.

What exactly does presque mean here, and where should it go?

Presque means “almost / nearly”.

Here it modifies the adjective vide:

Le tram est presque vide. = The tram is almost empty.

Its position is fixed right before what it modifies:

presque vide (almost empty)
presque toujours (almost always)
presque personne (almost no one)

You wouldn’t say est vide presque in this sentence; that’s not idiomatic.

Why is it le dimanche instead of just dimanche? What’s the difference?

Both exist, but they don’t mean exactly the same thing.

le dimanche = on Sundays (in general, habitually)
dimanche = this Sunday / on Sunday (usually referring to one specific Sunday, depending on context)

In your sentence:

…est presque vide le dimanche.
= It is almost empty on Sundays (as a general rule).

If you said:

…est presque vide dimanche.
it would more likely mean this coming Sunday it will be almost empty, depending on context.

So le dimanche fits well with d’habitude, both expressing a general habit.

Why do we use the present tense s’assoit to talk about a habitual action? Shouldn’t it be some “habitual tense”?

French uses the present tense for habits and repeated actions, just like English:

Elle s’assoit d’habitude dans ce tram.
= She usually sits in this tram.
Je prends toujours mon café à huit heures.
= I always have my coffee at 8.

There is no special “habitual tense” in French. The idea of habit is expressed with:

adverbs: d’habitude, souvent, toujours, tous les jours, etc.
time expressions: le dimanche, chaque matin, etc.

That’s exactly what happens in your sentence with d’habitude and le dimanche.