Learn Hardcore Portuguese (Brazil): Eu ainda não paguei o aluguel, mas vou pagar pelo aplicativo agora. - I still haven’t paid the rent, but I’m going to pay through the app now.

Yes, you can often omit it. Portuguese verb endings usually show the subject, so Ainda não paguei o aluguel... is natural and common.
Keeping Eu can add emphasis/contrast (e.g., I haven’t paid, maybe someone else has).

What does ainda não mean exactly, and how is it different from just não?

Ainda não means not yet: the action hasn’t happened up to now, but it’s expected to happen.
Não is just not and doesn’t include that “up to now / expected later” nuance.

Why is it não paguei (past) if the rent is still unpaid?

Portuguese commonly uses the pretérito perfeito (paguei) to talk about a completed action that didn’t happen in the relevant time frame: I didn’t pay (it).
With ainda não, it becomes “I haven’t paid it yet.” This is a very typical way to express what English often puts in the present perfect.

Is paguei the same as English I paid or I have paid?

Paguei is the pretérito perfeito and can match either English I paid or I have paid, depending on context.
In this sentence, with ainda não, it functions like I haven’t paid yet.

Why is there an article: o aluguel? Do I have to use o?

Portuguese often uses definite articles more than English does. Pagar o aluguel is the normal way to say pay the rent (the specific rent you owe).
You might omit the article in some contexts (especially in signs/headlines), but in everyday speech o aluguel sounds most natural.

What’s the difference between aluguel and renda?

In Brazil, aluguel is the standard word for rent (especially rent you pay for a place).
Renda usually means income/earnings. (In some other Portuguese varieties, renda can mean rent, but in Brazil that’s not the default.)

Why use mas here, and where does the comma go?

Mas = but. It contrasts two clauses: not paid yet vs. will pay now.
The comma before mas is standard in writing when it links two independent clauses: ..., mas ....

What does vou pagar express—future or intention?

Both. Vou pagar (literally “I’m going to pay”) is the common spoken way to express a near/planned future and intention.
It can sound more immediate than the simple future pagarei.

Could I say pagarei instead of vou pagar?

Yes, but it sounds more formal or written, and sometimes more “firm/official.”
In casual Brazilian Portuguese, vou pagar is usually more natural.

Why is it pelo aplicativo and not no aplicativo?

Pelo = por + o and here por means via / by means of: pay via the app.
No aplicativo (em + o) means in/on the app (location/context), which can also be possible, but it slightly shifts the idea to where the action happens rather than the method. Pelo aplicativo strongly emphasizes the method/channel.

What exactly is pelo grammatically?

It’s a contraction: por + o = pelo.
Similarly: por + a = pela, por + os = pelos, por + as = pelas.

Where does agora normally go in Portuguese? Could it be earlier in the sentence?

Agora is flexible. The sentence’s placement (...agora) is very natural and emphasizes “right now.”
You could also say: ...mas agora vou pagar pelo aplicativo. That puts extra focus on agora (now, as opposed to earlier).

Does aplicativo always mean a phone app? Could it be a desktop app?

In Brazil, aplicativo most commonly refers to a mobile app, but it can also mean an application/program more generally. Context usually makes it clear; with payments, people often assume a phone app or banking app.

How would pronunciation work for tricky parts like ainda, paguei, and pelo aplicativo?

A rough guide (Brazilian Portuguese):

ainda: the ai is like “eye,” and the -nda is nasal-ish: something like EYE-n-dah (with a nasal tone).
paguei: often sounds like pah-GAY (the final -ei is like “ay” in “say”).
pelo aplicativo: PEH-lo ah-plee-kah-TCHEE-vo (in many accents, ti can sound like chee).