Learn Farsi: اختصاصی‌ترین اسکله برای این ناوگان ساخته خواهد شد. - A most exclusive dock will be built for this fleet.

This is the absolute use of the superlative suffix -tarin. Instead of comparing the dock to all others in a specific group, the speaker is using the superlative to express an extreme, standalone degree of exclusivity. We often translate this absolute use into English with 'a most' or 'highly'.

Since the translation says 'a most exclusive dock', shouldn't there be an indefinite -i added to اسکله?

Not when using a superlative adjective before the noun. Adjectives ending in -tarin strictly precede the noun they modify, and that noun stays in its bare, singular form. The indefinite feel comes entirely from the absolute context of the superlative, so no extra suffix is needed on اسکله.

Why is the future tense verb خواهد شد preceded by ساخته rather than a standard verb stem?

This sentence is a great review of the passive voice in the future tense. To form the passive, Farsi uses the past participle of the main verb (here, ساخته from ساختن) followed by the conjugated auxiliary verb شدن. So ساخته خواهد شد literally means 'will become built'.

Does the word ناوگان have a plural suffix, or is that just how the root word ends?

ناوگان is a collective noun meaning 'fleet'. While it was historically formed using the suffix -gan (a variant of the plural suffix -an added to ناو, meaning ship or vessel), it functions in modern Farsi as a singular vocabulary word representing a whole group of ships or vehicles.